It would be convenient if REViewer could generate plots and metrics for all loci in a catalog by default.

Hi @egor-dolzhenko,
This is more of a combined REViewer/EH question.

I am trying to generate a Reviewer graph for a locus from RNASeq data. It runs until the plot blueprint stage and then generates the segmentation fault error.
[2021-11-08 17:42:57.730] [info] Loading specification of locus NIPA1
[2021-11-08 17:42:57.823] [info] Extracted 84 frags
[2021-11-08 17:42:57.823] [info] Calculating fragment length
[2021-11-08 17:42:57.824] [info] Fragment length is estimated to be 191
[2021-11-08 17:42:57.824] [info] Extracting genotype paths
[2021-11-08 17:42:57.826] [info] Phasing
[2021-11-08 17:42:57.830] [info] Found 2 paths defining genotype
[2021-11-08 17:42:57.830] [info] Projecting reads onto haplotype paths
[2021-11-08 17:42:57.831] [info] Projected 84 read pairs
[2021-11-08 17:42:57.831] [info] Generating fragment alignments
[2021-11-08 17:42:57.831] [info] Generated 84 fragment alignments
[2021-11-08 17:42:57.831] [info] Assigning fragment origins
[2021-11-08 17:42:57.833] [info] Found assignments for 84 frags
[2021-11-08 17:42:57.833] [info] Generating plot blueprint
Segmentation fault (core dumped)

Locus information from the ExpHunter run is as follows-
"NIPA1": {
"AlleleCount": 2,
"Coverage": 14.291508923742562,
"FragmentLength": 191,
"LocusId": "NIPA1",
"ReadLength": 151,
"Variants": {
"NIPA1": {
"CountsOfFlankingReads": "()",
"CountsOfInrepeatReads": "()",
"CountsOfSpanningReads": "()",
"Genotype": "0/0",
"GenotypeConfidenceInterval": "0-714/0-714",
"ReferenceRegion": "chr15:22786677-22786701",
"RepeatUnit": "GCG",
"VariantId": "NIPA1",
"VariantSubtype": "Repeat",
"VariantType": "Repeat"

If the lack of FR, IRR and SR is causing the error, then I wonder how the coverage for the loci was calculated.

Regards,
Hasna

Hi,

we have a case where there seems to be bug in REViewer.
The repeat units for C9ORF72 are 2/677 according to the VCF generated by ExpansionHunter 5.0.0:
chr9 27573528 . C , . PASS END=27573546;REF=3;RL=18;RU=GGCCCC;VARID=C9ORF72;REPID=C9ORF72 GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC 1/2:SPANNING/INREPEAT:2/677:2-2/628-970:27/0:7/41:0/612:57.641694

However when running REViewer 0.2.7 the SVG image shows 386 repeat units for the second allele:

This file should contain everything you need to replicate the issue:
REviewer_issue_.zip

If you need more information or data, I can provide that.

Best,
Marc

Note to me: it is in sample DNA2204013A1_02

Here is my command
../REViewer/build/install/bin/REViewer --reads example/output/repeats_realigned.srt.bam --vcf example/output/repeats.vcf --reference example/input/reference.fa --catalog example/input/variants.json --locus SNV_AND_STR --output-prefix test

Here is response
[2021-03-23 08:54:23.506] [info] Loading specification of locus SNV_AND_STR
[2021-03-23 08:54:23.537] [info] Extracted 549 frags
[2021-03-23 08:54:23.537] [info] Calculating fragment length
[2021-03-23 08:54:23.538] [info] Fragment length is estimated to be 351
[2021-03-23 08:54:23.538] [info] Extracting genotype paths
REViewer: /home/missionbio/REViewer/reviewer/app/GenotypePaths.cpp:106: std::map<std::pair<unsigned int, unsigned int>, std::vector<std::vector > > getVariantPathPieces(int, const string&, const LocusSpecification&): Assertion `variantSpec.classification().type == VariantType::kRepeat' failed.
Aborted (core dumped)

REViewer v0.2.1
ExpansionHunter v4.0.2 / v3.1.2/ v3.2.0

Like other ExpansionHunter tools, it was really easy to install and start using REViewer.
The one error I ran into was that the --vcf arg is required.
Also, it might be worth noting that the BAMlet generated by ExpansionHunter has to be sorted and indexed.

Hi Egor @egor-dolzhenko

I am using a bam file with manually selected paired end reads aligned with Repeat Unit (genomic location used as defined in the variant catalog) to generate a reviewer plot. We extracted these reads from the realigned bam file generated by Expansion Hunter.

I get the foll. error-

"Missing flanking read fragments"

What would this error message imply and is there a way to rectify this?

Heyo, I'm not very savvy with cpp so can't quite figure this one out on my own. Full error message:

REViewer-v0.2.7-linux_x86_64: app/GenotypePaths.cpp:119: std::map<std::pair<unsigned int, unsigned int>, std::vector<std::vector<unsigned int> > > getGenotypeNodesByNodeRange(int, const string&, const LocusSpecification&): Assertion `variantSpec.classification().type == VariantType::kRepeat' failed.
run_REViewer.scr: line 7:  7312 Aborted                 (core dumped) REViewer-v0.2.7-linux_x86_64 --reads repeats_realigned.sorted.bam --reference ../input/reference.fa --catalog ../input/variants.json --vcf repeats.vcf --locus SNV_AND_STR --output-prefix reviewer_out_

All the input files are identical to or derived from the example data bundled with the latest ExpansionHunter release. The only change is I sorted and indexed the bamlet with samtools.

Thanks in advance!

Hi and thank you for a very useful tool.
I installed the software a while ago without any problems but yesterday when trying a fresh install I got an error that the https://dl.bintray.com/boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2 was forbidden. The error is the same today. I appreciate if you would look into that.

Thank you.

Kind Regards,
Paul

I compiled version 0.27 and the head of the default branch. The output of the AlleleDepth differs: the total AlleleDepth is the same, but the first Allele always seems lower. A minor deviation was expected, but the variation is quite significant.

For example(variant names are renamed because of privacy concerns):

==> sampleX.metrics.tsv_0.2.7 <==

VariantId       Genotype        AlleleDepth
var1       4/4     16.44/15.44
var2       6/6     24.11/18.72
var3       4/4     28.38/25.75
var4 9/9     22.39/21.39
var5       4/4     15.75/16.95
var6       2/2     15.45/19.91

==> sampleX.metrics.tsv_head <==

VariantId       Genotype        AlleleDepth
var1       4/4     12.56/19.31
var2       6/6     19.39/23.44
var3       4/4     24.94/29.19
var4 9/9     18.22/25.56
var5       4/4     23.60/9.10
var6       2/2     19.82/15.55

The input files are identical. Both binaries were compiled with the same container(available upon request) and the binary of version V0.2.7 gives the same results as the static compiled version downloaded from Git Hub.

Which version should be considered the "gold standard"?

I ran into this error in the following run

REViewer --reads expansion_hunter4_realigned.sorted.bam --vcf expansion_hunter4.vcf --reference /gcsfuse_mounts/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta --catalog repeat_specs__all_pathogenic_loci_variant_catalog.json --locus chrX-25013649-25013697-CGC --output-prefix chrX-25013649-25013697-CGC_ExpansionHunter4
[2021-01-15 12:30:28.244] [info] Loading specification of locus chrX-25013649-25013697-CGC
[2021-01-15 12:30:28.586] [info] Extracted 99 frags
[2021-01-15 12:30:28.586] [info] Calculating fragment length
[2021-01-15 12:30:28.586] [info] Fragment length is estimated to be 352
[2021-01-15 12:30:28.586] [info] Extracting genotype paths
REViewer: /REViewer-master/reviewer/app/GenotypePaths.cpp:125: std::map<std::pair<unsigned int, unsigned int>, std::vector<std::vector<unsigned int> > > getVariantPathPieces(int, const string&, const LocusSpecification&): Assertion `variantPaths.size() == 2' failed.
/bin/bash: line 65:  1604 Aborted                 (core dumped) REViewer --reads expansion_hunter4_realigned.sorted.bam --vcf expansion_hunter4.vcf --reference /gcsfuse_mounts/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta --catalog /localized/gnomad-bw2/project1/ref/GRCh38/repeats_db/repeat_specs__all_pathogenic_loci_variant_catalog.json --locus chrX-25013649-25013697-CGC --output-prefix chrX-25013649-25013697-CGC-ExpansionHunter4

Bases shown despite matching the reference. Is this an indicator of low base quality score?

I am getting this error! what could be the reason?

How do we interpret the diplotype score outputted in phasing.tsv?
What does it mean, and how can we use it for QC filtering?

We are very used to having only compressed VCFs. While the ExHu-VCFs are tiny, it would be nifty if REViewer would read the compressed files as well, if via htslib or just libgz. Cheers, and thanks for the good work!

Hello again!

I am interested in how to create the correct pipeline consisted of EH + Stranger (big thx to @dnil) + REViewer that should work on test data at first.
I've taken variant catalog from the example as it follows https://github.com/Illumina/ExpansionHunter/blob/master/example/input/variants.json and had this one:
[error] Error loading locus SNV_AND_STR: Flanks can contain at most 5 characters N but found 2000 Ns.

Does REViewer work on test data from EH or I should take another example?

Thanks.

Hi Egor,

This issue is from Illumina/ExpansionHunter#150.

Thanks,
JaeHyun

Good morning,

Since the 1st May 2021 the website https://dl.bintray.com/ has not been supported; so, could u please change the download link for Boost app into the new one: https://boostorg.jfrog.io/artifactory/main/release ?

cause for now I get the following error while trying to launch REViewer:
Makefile:90: recipe for target 'all' failed make: *** [all] Error 2

Best wishes,
K

Hi Egor,
I am generating bamlets to generate plots using Reviewer to support Expansion hunter results. EH generates a new bam file with the extension "_realigned.bam". Is that the BAMlet?
Should I use that file or use my original bam file as input for makebamlet.py (EHDN) to make bamlets for my desired genes?
-Hasna

HI @egor-dolzhenko
I am trying to install REViewer in MACOS using the source file.
However, I am running into the foll. error. which is probably related with Boost libraries-

Scanning dependencies of target Boost
[ 42%] Creating directories for 'Boost'
[ 45%] Performing download step (download, verify and extract) for 'Boost'
-- Downloading...
dst='/Users/hasnahana/Downloads/REViewer-0.1.1/build/Boost-prefix/src/boost_1_73_0.tar.bz2'
timeout='none'
-- Using src='https://dl.bintray.com/boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2'
-- Retrying...
-- Using src='https://dl.bintray.com/boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2'
-- Retry after 5 seconds (attempt #2) ...
-- Using src='https://dl.bintray.com/boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2'
-- Retry after 5 seconds (attempt #3) ...
-- Using src='https://dl.bintray.com/boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2'
-- Retry after 15 seconds (attempt #4) ...
-- Using src='https://dl.bintray.com/boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2'
-- Retry after 60 seconds (attempt #5) ...
-- Using src='https://dl.bintray.com/boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2'
CMake Error at Boost-stamp/download-Boost.cmake:159 (message):
Each download failed!

error: downloading 'https://dl.bintray.com/boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2' failed
     status_code: 22
     status_string: "HTTP response code said error"
     log:
     --- LOG BEGIN ---
       Trying 52.38.32.109:443...

TCP_NODELAY set

Connected to dl.bintray.com (52.38.32.109) port 443 (#0)

ALPN, offering http/1.1

TLS 1.2 connection using TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256

ALPN, server did not agree to a protocol

Server certificate: *.bintray.com

Server certificate: GeoTrust RSA CA 2018

Server certificate: DigiCert Global Root CA

GET /boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2 HTTP/1.1

Host: dl.bintray.com

User-Agent: curl/7.65.0

Accept: /

Mark bundle as not supporting multiuse

The requested URL returned error: 403 Forbidden

Closing connection 0

     --- LOG END ---
     error: downloading 'https://dl.bintray.com/boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2' failed
     status_code: 22
     status_string: "HTTP response code said error"
     log:
     --- LOG BEGIN ---
       Trying 35.164.5.2:443...

TCP_NODELAY set

Connected to dl.bintray.com (35.164.5.2) port 443 (#0)

ALPN, offering http/1.1

TLS 1.2 connection using TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256

ALPN, server did not agree to a protocol

Server certificate: *.bintray.com

Server certificate: GeoTrust RSA CA 2018

Server certificate: DigiCert Global Root CA

GET /boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2 HTTP/1.1

Host: dl.bintray.com

User-Agent: curl/7.65.0

Accept: /

Mark bundle as not supporting multiuse

The requested URL returned error: 403 Forbidden

Closing connection 0

     --- LOG END ---
     error: downloading 'https://dl.bintray.com/boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2' failed
     status_code: 22
     status_string: "HTTP response code said error"
     log:
     --- LOG BEGIN ---
       Trying 35.164.5.2:443...

TCP_NODELAY set

Connected to dl.bintray.com (35.164.5.2) port 443 (#0)

ALPN, offering http/1.1

TLS 1.2 connection using TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256

ALPN, server did not agree to a protocol

Server certificate: *.bintray.com

Server certificate: GeoTrust RSA CA 2018

Server certificate: DigiCert Global Root CA

GET /boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2 HTTP/1.1

Host: dl.bintray.com

User-Agent: curl/7.65.0

Accept: /

Mark bundle as not supporting multiuse

The requested URL returned error: 403 Forbidden

Closing connection 0

     --- LOG END ---
     error: downloading 'https://dl.bintray.com/boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2' failed
     status_code: 22
     status_string: "HTTP response code said error"
     log:
     --- LOG BEGIN ---
       Trying 35.164.5.2:443...

TCP_NODELAY set

Connected to dl.bintray.com (35.164.5.2) port 443 (#0)

ALPN, offering http/1.1

TLS 1.2 connection using TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256

ALPN, server did not agree to a protocol

Server certificate: *.bintray.com

Server certificate: GeoTrust RSA CA 2018

Server certificate: DigiCert Global Root CA

GET /boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2 HTTP/1.1

Host: dl.bintray.com

User-Agent: curl/7.65.0

Accept: /

Mark bundle as not supporting multiuse

The requested URL returned error: 403 Forbidden

Closing connection 0

     --- LOG END ---
     error: downloading 'https://dl.bintray.com/boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2' failed
     status_code: 22
     status_string: "HTTP response code said error"
     log:
     --- LOG BEGIN ---
       Trying 35.164.5.2:443...

TCP_NODELAY set

Connected to dl.bintray.com (35.164.5.2) port 443 (#0)

ALPN, offering http/1.1

TLS 1.2 connection using TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256

ALPN, server did not agree to a protocol

Server certificate: *.bintray.com

Server certificate: GeoTrust RSA CA 2018

Server certificate: DigiCert Global Root CA

GET /boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2 HTTP/1.1

Host: dl.bintray.com

User-Agent: curl/7.65.0

Accept: /

Mark bundle as not supporting multiuse

The requested URL returned error: 403 Forbidden

Closing connection 0

     --- LOG END ---
     error: downloading 'https://dl.bintray.com/boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2' failed
     status_code: 22
     status_string: "HTTP response code said error"
     log:
     --- LOG BEGIN ---
       Trying 35.164.5.2:443...

TCP_NODELAY set

Connected to dl.bintray.com (35.164.5.2) port 443 (#0)

ALPN, offering http/1.1

TLS 1.2 connection using TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256

ALPN, server did not agree to a protocol

Server certificate: *.bintray.com

Server certificate: GeoTrust RSA CA 2018

Server certificate: DigiCert Global Root CA

GET /boostorg/release/1.73.0/source/boost_1_73_0.tar.bz2 HTTP/1.1

Host: dl.bintray.com

User-Agent: curl/7.65.0

Accept: /

Mark bundle as not supporting multiuse

The requested URL returned error: 403 Forbidden

Closing connection 0

     --- LOG END ---

make[2]: *** [Boost-prefix/src/Boost-stamp/Boost-download] Error 1
make[1]: *** [CMakeFiles/Boost.dir/all] Error 2
make: *** [all] Error 2

Hi there!

I'm trying to install this in my local space on an HPC and I'm getting this error both when I clone the repo and when I download the latest release:

make[4]: *** [thirdparty/graph-tools/CMakeFiles/graphtools.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [reviewer-prefix/src/reviewer-stamp/reviewer-build] Error 2
make[1]: *** [CMakeFiles/reviewer.dir/all] Error 2
make: *** [all] Error 2

I'm setting up the environment using conda. Any thoughts as to what is causing the error?

Thanks!
Sheina

Hi, I'm trying to visualize the repeat analyzed with ExpansionHunter.
However, whenever I try, the error below comes up and it doesn't work, even I specify ATN1 for locus

[error] Field LocusId must be present in {"LocusResults":{"ATN1":{"AlleleCount":2,"Coverage":18.405405405405403,"FragmentLength":545,"LocusId":"ATN1","ReadLength":150,"Variants":{"ATN1":{"CountsOfFlankingReads":"(3, 1), (5, 2), (8, 1), (9, 1), (10, 2), (11, 1), (14, 4), (17, 2), (18, 2)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(17, 1), (19, 9), (22, 5), (23, 1)","Genotype":"19/22","GenotypeConfidenceInterval":"19-19/22-22","ReferenceRegion":"chr12:6936716-6936773","RepeatUnit":"CAG","VariantId":"ATN1","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"ATXN1":{"AlleleCount":2,"Coverage":24.486486486486488,"FragmentLength":565,"LocusId":"ATXN1","ReadLength":150,"Variants":{"ATXN1":{"CountsOfFlankingReads":"(2, 1), (4, 1), (5, 1), (7, 1), (8, 2), (9, 3), (12, 2), (15, 2), (16, 1), (17, 2), (18, 1), (19, 2), (20, 1), (21, 4), (22, 2), (23, 1), (24, 2), (25, 2), (26, 2), (28, 1), (29, 2)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(29, 6), (30, 5)","Genotype":"29/30","GenotypeConfidenceInterval":"29-29/30-30","ReferenceRegion":"chr6:16327633-16327723","RepeatUnit":"TGC","VariantId":"ATXN1","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"ATXN10":{"AlleleCount":2,"Coverage":25.7027027027027,"FragmentLength":564,"LocusId":"ATXN10","ReadLength":150,"Variants":{"ATXN10":{"CountsOfFlankingReads":"(1, 4), (2, 4), (3, 3), (5, 2), (6, 4), (7, 4), (8, 2), (9, 1), (10, 1), (11, 3), (12, 2), (13, 7), (14, 1)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(7, 1), (14, 10), (16, 7)","Genotype":"14/16","GenotypeConfidenceInterval":"14-14/16-16","ReferenceRegion":"chr22:45795354-45795424","RepeatUnit":"ATTCT","VariantId":"ATXN10","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"ATXN3":{"AlleleCount":2,"Coverage":27.486486486486484,"FragmentLength":553,"LocusId":"ATXN3","ReadLength":150,"Variants":{"ATXN3":{"CountsOfFlankingReads":"(1, 1), (2, 1), (3, 1), (6, 1), (7, 3), (8, 2), (9, 1), (13, 2), (14, 1), (15, 3), (16, 1)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(11, 13), (16, 12)","Genotype":"11/16","GenotypeConfidenceInterval":"11-11/16-16","ReferenceRegion":"chr14:92071009-92071042","RepeatUnit":"GCT","VariantId":"ATXN3","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"ATXN7":{"AlleleCount":2,"Coverage":12.81081081081081,"FragmentLength":551,"LocusId":"ATXN7","ReadLength":150,"Variants":{"ATXN7":{"CountsOfFlankingReads":"(4, 1), (6, 1), (7, 2), (9, 2)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(0, 1), (2, 1), (10, 10)","Genotype":"10/10","GenotypeConfidenceInterval":"10-10/10-10","ReferenceRegion":"chr3:63912684-63912714","RepeatUnit":"GCA","VariantId":"ATXN7","VariantSubtype":"Repeat","VariantType":"Repeat"},"ATXN7_GCC":{"CountsOfFlankingReads":"(1, 1), (2, 2), (3, 1)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(4, 14)","Genotype":"4/4","GenotypeConfidenceInterval":"4-4/4-4","ReferenceRegion":"chr3:63912714-63912726","RepeatUnit":"GCC","VariantId":"ATXN7_GCC","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"ATXN8OS":{"AlleleCount":2,"Coverage":32.67567567567568,"FragmentLength":546,"LocusId":"ATXN8OS","ReadLength":150,"Variants":{"ATXN8OS":{"CountsOfFlankingReads":"(1, 1), (2, 5), (3, 2), (5, 1), (7, 1), (8, 1), (9, 2), (11, 4), (12, 1), (13, 2), (14, 1), (15, 2), (16, 3), (18, 1), (20, 1), (21, 1)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(14, 1), (15, 13), (23, 11)","Genotype":"15/23","GenotypeConfidenceInterval":"15-15/23-23","ReferenceRegion":"chr13:70139383-70139428","RepeatUnit":"CTG","VariantId":"ATXN8OS","VariantSubtype":"Repeat","VariantType":"Repeat"},"ATXN8OS_CTA":{"CountsOfFlankingReads":"(2, 2), (3, 1), (4, 3), (6, 1), (7, 1), (9, 1)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(8, 16), (9, 20)","Genotype":"8/9","GenotypeConfidenceInterval":"8-8/9-9","ReferenceRegion":"chr13:70139353-70139383","RepeatUnit":"CTA","VariantId":"ATXN8OS_CTA","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"C9ORF72":{"AlleleCount":2,"Coverage":20.35135135135135,"FragmentLength":547,"LocusId":"C9ORF72","ReadLength":150,"Variants":{"C9ORF72":{"CountsOfFlankingReads":"(1, 1)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(2, 32)","Genotype":"2/2","GenotypeConfidenceInterval":"2-2/2-2","ReferenceRegion":"chr9:27573528-27573546","RepeatUnit":"GGCCCC","VariantId":"C9ORF72","VariantSubtype":"RareRepeat","VariantType":"Repeat"}}},"CACNA1A":{"AlleleCount":2,"Coverage":19.945945945945947,"FragmentLength":511,"LocusId":"CACNA1A","ReadLength":150,"Variants":{"CACNA1A":{"CountsOfFlankingReads":"(1, 1), (2, 1), (3, 1), (4, 1), (5, 1), (7, 3), (9, 2), (10, 2)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(13, 17)","Genotype":"13/13","GenotypeConfidenceInterval":"13-13/13-13","ReferenceRegion":"chr19:13207858-13207897","RepeatUnit":"CTG","VariantId":"CACNA1A","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"CBL":{"AlleleCount":2,"Coverage":17.513513513513512,"FragmentLength":541,"LocusId":"CBL","ReadLength":150,"Variants":{"CBL":{"CountsOfFlankingReads":"(2, 1), (4, 2), (7, 1), (8, 1), (9, 1), (10, 1)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(11, 24)","Genotype":"11/11","GenotypeConfidenceInterval":"11-11/11-11","ReferenceRegion":"chr11:119206289-119206322","RepeatUnit":"CGG","VariantId":"CBL","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"CNBP":{"AlleleCount":2,"Coverage":25.62162162162162,"FragmentLength":570,"LocusId":"CNBP","ReadLength":150,"Variants":{"CNBP":{"CountsOfFlankingReads":"(1, 1), (2, 3), (3, 1), (4, 2), (6, 2), (7, 4), (10, 1), (15, 3), (19, 1)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(15, 14), (16, 1), (19, 7)","Genotype":"15/19","GenotypeConfidenceInterval":"15-15/19-19","ReferenceRegion":"chr3:129172576-129172656","RepeatUnit":"CAGG","VariantId":"CNBP","VariantSubtype":"Repeat","VariantType":"Repeat"},"CNBP_CA":{"CountsOfFlankingReads":"(3, 1), (4, 2), (5, 1), (6, 1), (7, 2), (8, 1), (9, 1), (10, 2), (11, 1), (14, 1), (15, 3), (17, 2), (18, 3), (19, 2), (20, 1), (23, 1)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(20, 2), (22, 7), (24, 1)","Genotype":"20/22","GenotypeConfidenceInterval":"20-20/22-22","ReferenceRegion":"chr3:129172696-129172732","RepeatUnit":"CA","VariantId":"CNBP_CA","VariantSubtype":"Repeat","VariantType":"Repeat"},"CNBP_CAGA":{"CountsOfFlankingReads":"(1, 1), (2, 2), (4, 1), (6, 1), (8, 1), (9, 1), (10, 5)","CountsOfInrepeatReads":"(2, 1)","CountsOfSpanningReads":"(2, 9), (9, 1), (10, 10)","Genotype":"2/10","GenotypeConfidenceInterval":"2-2/10-10","ReferenceRegion":"chr3:129172656-129172696","RepeatUnit":"CAGA","VariantId":"CNBP_CAGA","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"CSTB":{"AlleleCount":2,"Coverage":18.56756756756757,"FragmentLength":553,"LocusId":"CSTB","ReadLength":150,"Variants":{"CSTB":{"CountsOfFlankingReads":"(1, 3), (2, 4)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(2, 13), (3, 14)","Genotype":"2/3","GenotypeConfidenceInterval":"2-2/3-3","ReferenceRegion":"chr21:43776443-43776479","RepeatUnit":"CGCGGGGCGGGG","VariantId":"CSTB","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"DIP2B":{"AlleleCount":2,"Coverage":22.054054054054053,"FragmentLength":551,"LocusId":"DIP2B","ReadLength":150,"Variants":{"DIP2B":{"CountsOfFlankingReads":"(1, 2), (4, 1), (5, 1), (7, 1)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(7, 18)","Genotype":"7/7","GenotypeConfidenceInterval":"7-7/7-7","ReferenceRegion":"chr12:50505001-50505022","RepeatUnit":"GGC","VariantId":"DIP2B","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"DMPK":{"AlleleCount":2,"Coverage":21.486486486486488,"FragmentLength":528,"LocusId":"DMPK","ReadLength":150,"Variants":{"DMPK":{"CountsOfFlankingReads":"(2, 1), (3, 1), (5, 1), (7, 1), (8, 1), (9, 1), (10, 1), (11, 2)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(5, 11), (13, 8)","Genotype":"5/13","GenotypeConfidenceInterval":"5-5/13-13","ReferenceRegion":"chr19:45770204-45770264","RepeatUnit":"CAG","VariantId":"DMPK","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"FXN":{"AlleleCount":2,"Coverage":21.243243243243242,"FragmentLength":535,"LocusId":"FXN","ReadLength":150,"Variants":{"FXN":{"CountsOfFlankingReads":"(1, 2), (2, 3), (3, 1), (5, 4), (6, 1), (9, 1)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(8, 7), (9, 9)","Genotype":"8/9","GenotypeConfidenceInterval":"8-8/9-9","ReferenceRegion":"chr9:69037286-69037304","RepeatUnit":"GAA","VariantId":"FXN","VariantSubtype":"Repeat","VariantType":"Repeat"},"FXN_A":{"CountsOfFlankingReads":"(4, 1), (14, 1), (17, 1), (20, 2), (21, 1), (27, 1), (38, 1)","CountsOfInrepeatReads":"(13, 1), (63, 1)","CountsOfSpanningReads":"(4, 3), (15, 1), (19, 1), (26, 1), (27, 15), (30, 1), (31, 1), (128, 1)","Genotype":"27/150","GenotypeConfidenceInterval":"27-27/58-259","ReferenceRegion":"chr9:69037261-69037286","RepeatUnit":"A","VariantId":"FXN_A","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"GIPC1":{"AlleleCount":2,"Coverage":19.864864864864867,"FragmentLength":536,"LocusId":"GIPC1","ReadLength":150,"Variants":{"GIPC1":{"CountsOfFlankingReads":"(1, 1), (2, 1), (3, 1), (4, 1), (7, 1), (9, 3), (11, 1), (12, 1)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(11, 1), (12, 22)","Genotype":"12/12","GenotypeConfidenceInterval":"12-12/12-12","ReferenceRegion":"chr19:14496041-14496074","RepeatUnit":"CCG","VariantId":"GIPC1","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"GLS":{"AlleleCount":2,"Coverage":23.513513513513516,"FragmentLength":559,"LocusId":"GLS","ReadLength":150,"Variants":{"GLS":{"CountsOfFlankingReads":"(1, 1), (2, 2), (3, 3), (4, 1), (5, 2), (8, 1), (10, 1), (11, 1), (12, 4), (16, 1), (18, 2), (19, 1)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(15, 11), (19, 8), (20, 1)","Genotype":"15/19","GenotypeConfidenceInterval":"15-15/19-19","ReferenceRegion":"chr2:190880872-190880920","RepeatUnit":"GCA","VariantId":"GLS","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"HTT":{"AlleleCount":2,"Coverage":21.243243243243242,"FragmentLength":531,"LocusId":"HTT","ReadLength":150,"Variants":{"HTT":{"CountsOfFlankingReads":"(2, 1), (3, 2), (4, 2), (5, 1), (6, 1), (7, 1), (8, 1), (9, 1), (11, 1), (14, 5), (15, 1), (16, 3), (17, 2), (19, 1), (20, 2)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(16, 1), (17, 7), (20, 8)","Genotype":"17/20","GenotypeConfidenceInterval":"17-17/20-20","ReferenceRegion":"chr4:3074876-3074933","RepeatUnit":"CAG","VariantId":"HTT","VariantSubtype":"Repeat","VariantType":"Repeat"},"HTT_CCG":{"CountsOfFlankingReads":"(1, 3), (5, 2), (6, 1), (7, 3), (8, 1), (9, 1), (10, 1), (11, 4), (12, 3)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(12, 17)","Genotype":"12/12","GenotypeConfidenceInterval":"12-12/12-12","ReferenceRegion":"chr4:3074939-3074966","RepeatUnit":"CCG","VariantId":"HTT_CCG","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"JPH3":{"AlleleCount":2,"Coverage":22.864864864864863,"FragmentLength":571,"LocusId":"JPH3","ReadLength":150,"Variants":{"JPH3":{"CountsOfFlankingReads":"(1, 1), (2, 1), (4, 1), (7, 1), (8, 1), (9, 2), (11, 2), (12, 1), (13, 1)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(14, 14), (15, 9)","Genotype":"14/15","GenotypeConfidenceInterval":"14-14/15-15","ReferenceRegion":"chr16:87604287-87604329","RepeatUnit":"CTG","VariantId":"JPH3","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"NIPA1":{"AlleleCount":2,"Coverage":16.62162162162162,"FragmentLength":575,"LocusId":"NIPA1","ReadLength":150,"Variants":{"NIPA1":{"CountsOfFlankingReads":"(1, 1), (2, 1), (4, 1)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(3, 1), (5, 1), (8, 14)","Genotype":"8/8","GenotypeConfidenceInterval":"8-8/8-8","ReferenceRegion":"chr15:22786677-22786701","RepeatUnit":"GCG","VariantId":"NIPA1","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"NOP56":{"AlleleCount":2,"Coverage":23.513513513513516,"FragmentLength":543,"LocusId":"NOP56","ReadLength":150,"Variants":{"NOP56":{"CountsOfFlankingReads":"(2, 1), (3, 2), (4, 2), (5, 3), (6, 3), (8, 3)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(7, 10), (8, 16)","Genotype":"7/8","GenotypeConfidenceInterval":"7-7/8-8","ReferenceRegion":"chr20:2652733-2652757","RepeatUnit":"GGCCTG","VariantId":"NOP56","VariantSubtype":"Repeat","VariantType":"Repeat"},"NOP56_CGCCTG":{"CountsOfFlankingReads":"(1, 1), (2, 5)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(2, 28)","Genotype":"2/2","GenotypeConfidenceInterval":"2-2/2-2","ReferenceRegion":"chr20:2652757-2652775","RepeatUnit":"CGCCTG","VariantId":"NOP56_CGCCTG","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"NOTCH2NL":{"AlleleCount":2,"Coverage":17.594594594594593,"FragmentLength":557,"LocusId":"NOTCH2NL","ReadLength":150,"Variants":{"NOTCH2NL":{"CountsOfFlankingReads":"(1, 2), (3, 2), (4, 1), (5, 1), (6, 1), (7, 1), (8, 2), (10, 2), (13, 1)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(1, 1), (9, 5), (15, 7)","Genotype":"9/15","GenotypeConfidenceInterval":"9-9/15-15","ReferenceRegion":"chr1:149390802-149390841","RepeatUnit":"GGC","VariantId":"NOTCH2NL","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"PABPN1":{"AlleleCount":2,"Coverage":17.83783783783784,"FragmentLength":535,"LocusId":"PABPN1","ReadLength":150,"Variants":{"PABPN1":{"CountsOfFlankingReads":"(2, 1), (3, 1), (4, 2), (5, 1), (6, 1), (15, 1)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(5, 1), (6, 18)","Genotype":"6/6","GenotypeConfidenceInterval":"6-6/6-6","ReferenceRegion":"chr14:23321472-23321490","RepeatUnit":"GCG","VariantId":"PABPN1","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"PHOX2B":{"AlleleCount":2,"Coverage":15.486486486486486,"FragmentLength":552,"LocusId":"PHOX2B","ReadLength":150,"Variants":{"PHOX2B":{"CountsOfFlankingReads":"(1, 1), (2, 1), (3, 1), (4, 4), (6, 1), (7, 1), (8, 1), (10, 1), (11, 1), (13, 2), (14, 1), (19, 4), (20, 1)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(20, 6), (34, 1)","Genotype":"20/20","GenotypeConfidenceInterval":"20-20/20-23","ReferenceRegion":"chr4:41745972-41746032","RepeatUnit":"GCN","VariantId":"PHOX2B","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"PPP2R2B":{"AlleleCount":2,"Coverage":22.702702702702705,"FragmentLength":550,"LocusId":"PPP2R2B","ReadLength":150,"Variants":{"PPP2R2B":{"CountsOfFlankingReads":"(3, 3), (5, 2), (6, 1), (7, 1), (8, 1), (9, 5), (10, 1), (12, 1), (13, 2)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(10, 17), (16, 7)","Genotype":"10/16","GenotypeConfidenceInterval":"10-10/16-16","ReferenceRegion":"chr5:146878727-146878757","RepeatUnit":"GCT","VariantId":"PPP2R2B","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"RFC1":{"AlleleCount":2,"Coverage":25.135135135135137,"FragmentLength":548,"LocusId":"RFC1","ReadLength":150,"Variants":{"RFC1":{"CountsOfFlankingReads":"(2, 4), (3, 3), (4, 2), (5, 1), (6, 3), (7, 1), (8, 2), (9, 6), (10, 1), (12, 1), (14, 1), (15, 1), (16, 1), (17, 1), (18, 1), (20, 1), (21, 1), (22, 2), (23, 2), (26, 1), (27, 1), (28, 2)","CountsOfInrepeatReads":"(30, 24), (31, 4)","CountsOfSpanningReads":"(10, 9)","Genotype":"10/88","GenotypeConfidenceInterval":"10-10/69-124","ReferenceRegion":"chr4:39348424-39348479","RepeatUnit":"AARRG","VariantId":"RFC1","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"TBP":{"AlleleCount":2,"Coverage":28.135135135135133,"FragmentLength":540,"LocusId":"TBP","ReadLength":150,"Variants":{"TBP":{"CountsOfFlankingReads":"(1, 3), (2, 1), (3, 2), (4, 2), (5, 1), (7, 1), (9, 1), (10, 1), (11, 1), (12, 1), (13, 1), (16, 2), (17, 1), (19, 2), (20, 3), (22, 2), (25, 1), (26, 4), (27, 1), (30, 1), (33, 1), (36, 2)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(4, 2), (5, 1), (6, 2), (16, 1), (32, 5), (36, 1)","Genotype":"32/36","GenotypeConfidenceInterval":"32-32/36-47","ReferenceRegion":"chr6:170561906-170562017","RepeatUnit":"GCA","VariantId":"TBP","VariantSubtype":"Repeat","VariantType":"Repeat"}}},"TCF4":{"AlleleCount":2,"Coverage":22.702702702702705,"FragmentLength":576,"LocusId":"TCF4","ReadLength":150,"Variants":{"TCF4":{"CountsOfFlankingReads":"(1, 2), (2, 3), (3, 2), (5, 1), (6, 1), (7, 3), (9, 1), (10, 1), (11, 3), (13, 1), (14, 2), (15, 1), (18, 1), (20, 2), (21, 3), (23, 3), (24, 1), (25, 2), (26, 1), (32, 2)","CountsOfInrepeatReads":"()","CountsOfSpanningReads":"(19, 1), (26, 6), (29, 7)","Genotype":"26/29","GenotypeConfidenceInterval":"26-26/29-29","ReferenceRegion":"chr18:55586155-55586227","RepeatUnit":"CAG","VariantId":"TCF4","VariantSubtype":"Repeat","VariantType":"Repeat"}}}},"SampleParameters":{"SampleId":"DA0000005225","Sex":"Female"}}

Thank you in advance

Hi Egor,

I have a request for a new QC metric that would be analogous to the 'Fisher Strand' metric in GATK (https://gatk.broadinstitute.org/hc/en-us/articles/360040096152-FisherStrand). Basically, one would expect an even ratio of forward and reverse reads to be assigned to each of the two alleles at an STR site, but if there is a bias toward one of those directionalities on one of the alleles, it could indicate a low quality call.

Thanks again for all the great work you are doing on these tools!

Best,
Matt

Hi,

It would be really useful to have an option to display degenerate base pairs in the images generated by REViewer.

For example, this would help to distinguish AAAAG / AAGGG repeats at the RFC1 locus when reviewing these images

I ran EHv4 on the FXN locus, using 2 repeat specs which are identical except that the 2nd one includes GAA off-target regions:

{
        "LocusId": "FXN-chr9-69037286-69037304-GAA",
        "LocusStructure": "(GAA)*",
	"RepeatUnit": "GAA",
        "ReferenceRegion": "chr9:69037286-69037304",
        "VariantType": "RareRepeat",
	"OfftargetRegions": []
    },
    {
        "LocusId": "FXN-chr9-69037286-69037304-GAA-with-off-targets",
        "LocusStructure": "(GAA)*",
	"RepeatUnit": "GAA",
        "ReferenceRegion": "chr9:69037286-69037304",
        "VariantType": "RareRepeat",
	"OfftargetRegions": [
	    "chr2:220546033-220546610",
	    "chr5:127247161-127247640",
	    "chrX:51621350-51621856",
	    "chr1:101657701-101658187",
	    "chr13:102161416-102161881",
	    "chr7:37848005-37848522",
	    "chrY:25645531-25646013",
	    "chr7:84690949-84691442",
	    "chrUn_KN707747v1_decoy:1062-2074",
	    "chr6:50708070-50708556",
	    "chrY:24024122-24024600"
	]
    },

These are the EHv4 results in the (relatively rare) WGS sample where the genotypes from the 2 specs differed significantly between no-off-targets:

chr9	69037286	.	A	<STR9>,<STR110>	.	PASS	END=69037304;REF=6;RL=18;RU=GAA;VARID=FXN-chr9-69037286-69037304-GAA;REPID=FXN-chr9-69037286-69037304-GAA	GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC	1/2:SPANNING/INREPEAT:9/110:9-10/63-153:2/0:5/13:0/12:42.016851

and with off-targets:

chr9	69037286	.	A	<STR33>,<STR726>	.	PASS	END=69037304;REF=6;RL=18;RU=GAA;VARID=FXN-chr9-69037286-69037304-GAA-with-0.01-threshold-off-targets;REPID=FXN-chr9-69037286-69037304-GAA-with-0.01-threshold-off-targets	GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC	1/2:FLANKING/INREPEAT:33/726:33-111/658-1313:0/0:13/13:4/108:42.016851

I then ran REViewer for both outputs, and got these plots

no-off-targets:

with-off-targets:

finally, this is the plot from when I used the standard FXN repeat spec included in the EHv4 repo:

I'm wondering how to interpret the "with-off-targets plot". In REViewer docs, I saw
..the current version of REViewer visualizes repeats whose span does not exceed the fragment length (longer repeats are capped at the fragment length).
Does REViewer not plot the off-target FRRs?

Thanks
-Ben

Output phasing info into txt or csv file.

Encountering an issue while installing.

82%] Performing configure step for 'reviewer'
CMake Error at /usr/local/share/cmake-3.20/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
Could NOT find CURL (missing: CURL_LIBRARY CURL_INCLUDE_DIR)
Call Stack (most recent call first):
/usr/local/share/cmake-3.20/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE)
/usr/local/share/cmake-3.20/Modules/FindCURL.cmake:181 (find_package_handle_standard_args)
CMakeLists.txt:20 (find_package)

-- Configuring incomplete, errors occurred!
See also "/home/sngene1/REViewer/build/reviewer-prefix/src/reviewer-build/CMakeFiles/CMakeOutput.log".
make[2]: *** [CMakeFiles/reviewer.dir/build.make:91: reviewer-prefix/src/reviewer-stamp/reviewer-configure] Error 1
make[1]: *** [CMakeFiles/Makefile2:94: CMakeFiles/reviewer.dir/all] Error 2
make: *** [Makefile:91: all] Error 2

Please add a link to
https://www.illumina.com/science/genomics-research/reviewer-visualizing-alignments-short-reads-long-repeat.html
I keep having to go back to twitter to find it!

Hello, I keep getting this error, I've tried with three different loci, the error remains the same.

"LocusResults": {
    "AFF2": {
      "AlleleCount": 2,
      "Coverage": 31.54054054054054,
      "FragmentLength": 352,
      "LocusId": "AFF2",
      "ReadLength": 150,
      "Variants": {
        "AFF2": {
          "CountsOfFlankingReads": "()",
          "CountsOfInrepeatReads": "()",
          "CountsOfSpanningReads": "()",
          "Genotype": "0/0",
          "GenotypeConfidenceInterval": "0-714/0-714",
          "ReferenceRegion": "X:147582151-147582211",
          "RepeatUnit": "GCC",
          "VariantId": "AFF2",
          "VariantSubtype": "Repeat",
          "VariantType": "Repeat"
        }
      }
    },

"AR": {
      "AlleleCount": 2,
      "Coverage": 41.91891891891891,
      "FragmentLength": 350,
      "LocusId": "AR",
      "ReadLength": 150,
      "Variants": {
        "AR": {
          "CountsOfFlankingReads": "(1, 2), (2, 2), (3, 3), (4, 1), (5, 1), (6, 2), (8, 6), (9, 1), (10, 3), (15, 3), (17, 1), (18, 3), (19, 5), (20, 2), (23, 1), (24, 1), (26, 1), (28, 1)",
          "CountsOfInrepeatReads": "()",
          "CountsOfSpanningReads": "(27, 16), (28, 9)",
          "Genotype": "27/28",
          "GenotypeConfidenceInterval": "27-27/28-28",
          "ReferenceRegion": "X:66765158-66765227",
          "RepeatUnit": "GCA",
          "VariantId": "AR",
          "VariantSubtype": "Repeat",
          "VariantType": "Repeat"
        }
      }
    },

I thought maybe the problem was that there are no InrepeatReads, but the problem remains if only using an entry where all three read categories have members, e.g:

"LocusResults": {
    "RFC1": {
      "AlleleCount": 2,
      "Coverage": 41.513513513513516,
      "FragmentLength": 351,
      "LocusId": "RFC1",
      "ReadLength": 150,
      "Variants": {
        "RFC1": {
          "CountsOfFlankingReads": "(1, 2), (2, 2), (3, 3), (4, 2), (5, 2), (7, 2), (8, 5), (10, 2), (11, 1), (15, 1), (16, 1), (17, 2), (20, 1), (21, 1), (22, 1), (25, 1), (29, 4)",
          "CountsOfInrepeatReads": "(30, 15), (31, 1), (32, 1)",
          "CountsOfSpanningReads": "(10, 11), (15, 1)",
          "Genotype": "10/65",
          "GenotypeConfidenceInterval": "10-10/53-102",
          "ReferenceRegion": "4:39350044-39350099",
          "RepeatUnit": "AARRG",
          "VariantId": "RFC1",
          "VariantSubtype": "Repeat",
          "VariantType": "Repeat"
        }
      }
    }
  }

[2022-03-25 14:42:00.258] [info] Loading specification of locus RFC1
[2022-03-25 14:42:00.260] [error] Failed to extract reads from the specified region

What to do? :-(

REViewer-v0.2.7-linux_x86_64\
	--reads "$out"/exphout_"${sample}"_realigned.sorted.bam\
	--reference "$genome"\
	--catalog "$catalog"\
	--vcf exphout_"${sample}".vcf\
	--locus "RFC1"\
	--output-prefix "$out"/reviewerout_"${sample}"

Grateful for help with this! Am excited to see the pretty diagrams...

CMake Error at CMakeLists.txt:23 (find_package):
By not providing "Findfmt.cmake" in CMAKE_MODULE_PATH this project has
asked CMake to find a package configuration file provided by "fmt", but
CMake did not find one.

Could not find a package configuration file provided by "fmt" with any of
the following names:

fmtConfig.cmake
fmt-config.cmake

Add the installation prefix of "fmt" to CMAKE_PREFIX_PATH or set "fmt_DIR"
to a directory containing one of the above files. If "fmt" provides a
separate development package or SDK, be sure it has been installed.

Hello!

I have a problem while executing the main command. Option --locus as far as I understood requires an appropriate string of LocusID from the EH's outfile. For instance, as it follows in my result file (.json) (a fragment):
.. }, "ATXN10": { "AlleleCount": 2, "Coverage": 0.32432432432432434, "FragmentLength": 215, "LocusId": "ATXN10", "ReadLength": 150, "Variants": { "ATXN10": { "CountsOfFlankingReads": "()", "CountsOfInrepeatReads": "()", "CountsOfSpanningReads": "()", "ReferenceRegion": "chr22:46191234-46191304", "RepeatUnit": "ATTCT", "VariantId": "ATXN10", "VariantSubtype": "Repeat", "VariantType": "Repeat" } } ..
I tried to paste ATXN10 as an argument of --locus option, but have not gotten any success.

*btw, I have looked at Issue #2, particularly at the type of command from bw2. In his/her case, he/she got the EH's outfile with specified contig name and coordinates in LocusID:
"LocusId": "FXN-chr9-69037286-69037304-GAA". That makes me worried about that: possibly my outfile from EH is wrong?

Thank you so much!

For LocusStructures that contain 'N' or IUPAC bases like 'ARRGG', it would nice to see which bases are actually present in the reads at those positions. For example

knowing which bases are underneath the N positions would make it easier to check consistency with parental genotypes.

Hi

When I ran the command, the error message showed as below.

What did this mean? Could you please give me any suggestion?

Thanks

Sorry, I used to apply GraphAlignmentViewer for STR visualization.
So, what is the difference between GraphAlignmentViewer and REViewer?
Thank you!

Does REViewer work with ExpansionHunterDeNovo as well as ExpansionHunter?

I got this error on one out of ~300 samples. When I ran

REViewer --reads CDS-ulp4x8.expansion_hunter4_realigned.sorted.bam --vcf CDS-ulp4x8.expansion_hunter4.vcf --reference hg38.fa --catalog ./FXN_variant_catalog_with_0.01_threshold_off_targets.json --locus  FXN-chr9-69037286-69037304-GAA --output-prefix CDS-ulp4x8_FXN-chr9-69037286-69037304-GAA_ExpansionHunter4

the output was

[2021-01-10 18:14:17.325] [info] Loading specification of locus FXN-chr9-69037286-69037304-GAA
[2021-01-10 18:14:17.389] [info] Extracted 79 frags
[2021-01-10 18:14:17.389] [info] Calculating fragment length
[2021-01-10 18:14:17.389] [info] Fragment length is estimated to be 171
[2021-01-10 18:14:17.389] [info] Extracting genotype paths
[2021-01-10 18:14:17.393] [error] stoi: no conversion

for these input files:
files.zip

Hi,

our variant catalog contains OfftargetRegions on alternate contigs, e.g. "chr4_KI270790v1_alt:200469-201085"

ExpansionHunter works without issues and i get a valid vcf-file.

When starting REviewer with the exact same assembly reference and catalog, i get the error:

[error] Invalid contig name chr4_KI270790v1_alt

Removing all alt. contigs from the catalog results in the error:
[error] Failed to extract reads from the specified region

This is the catalog file: variant_catalog_gnomAD_with_offtargets.GRCh38_202306.json

Looking at REViewer plots, I start wondering whether particular reads that contradict or support a give genotype are low quality. It might be useful if REViewer could (optionally?) draw extra info like:

• plotting some number for each read that describes mapping quality
• showing read pairs rather than reads
• whether a mate or a read pair was recovered from a distant locus
• read strand

hi，all
when I run REViewer，the error is presented as follows：

my bam file is generated by minimap2 and when I added XG:i:0 to bam file，it showed "Unexpected auxiliary tag XG:C"

So what does the "XG" tag mean? how do I get it？

Looking forward to your reply. Thank you.

Good day,

Thank you so much for the tools!
I've constructed the pipeline consisted of EH -> .. -> REViewer and got the problem that both EH and REViewer install the same soft and packages (for instance, Boost). Moreover, I've installed them on my own. It would be great to skip a soft installation step in cases when it is already done.

Hello,

I get an error message when I try to run REViewer and I don't understand why. All files are present and seem to be complete. I have sorted and indexed my BAM. Thank you by advance for your help.

./REViewer-v0.2.7-linux_x86_64 --reads results/19A5405_realigned_sorted.bam --vcf results/19A5405.vcf --reference /srv/nfs/disnap/NGS/bioInfo/Bases_de_donnees/GRCh37_decoy/GRCh37Decoy.fasta --catalog CSTB.json --locus CSTB --output-prefix results/19A5405
[2023-09-21 15:43:32.147] [info] Loading specification of locus CSTB
[2023-09-21 15:43:32.159] [error] Failed to extract reads from the specified region

cat CSTB.json
[
    {
        "LocusId": "CSTB",
        "LocusStructure": "(CGCGGGGCGGGG)*",
        "ReferenceRegion": "chr21:45196324-45196360",
        "VariantType": "Repeat"
    }
]

samtools view results/19A5405_realigned_sorted.bam chr21:45196324-45196360 | head
NL500104:777:HCM3GAFX5:3:11502:24673:4992       77      chr21 45196325  0  *    *       0       0       CGCGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCTGGGTCTCCGCGCCCAGCGCTGGTGTCGGGAGGGAGCG     IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII!IIIIIIIIIIIIIIIIII!IIIIIIIIIIIIIIIIIIIIII   XG:Z:CSTB,0,1[12M]2[1M1X61M]
NL500104:777:HCM3GAFX5:3:11401:3971:20320       77      chr21 45196325  0  *    *       0       0       CGCGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCTGGGTCTCCGCGCCCGGCGCTGGTGTCGGGAGGGAGCG     IIIIIIIIIIII!IIIIIIII!II!IIIIIIII!III!IIIIIIIIIIIIII!IIIIIIIIIIIIIIIIII!III   XG:Z:CSTB,0,1[12M]2[1M1X38M1X22M]
NL500104:777:HCM3GAFX5:3:11407:21027:17686      125     chr21 45196325  0  *    *       0       0       GCGCGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCTGGGTCTCCGCGCCCAGCGCTGGTGTCGGGAGGGAGC     III!IIIIIIIIIIIII!IIIIIIIIIIIIIIIIIIIIIIII!IIIIIIII!IIIIIII!I!IIIIIIII!III!   XG:Z:CSTB,0,1[1S12M]2[1M1X60M]
NL500104:777:HCM3GAFX5:2:11211:22012:2769       125     chr21 45196325  0  *    *       0       0       CGCGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCTGGGTCTCCGCGCCCAGCGCTGGTGTCGGGAGGGAGCG     !I!IIII!IIIIIIII!IIII!IIIIIIIIIIIIIII!IIIIIIIIIIIIIIIIIII!IIIIIIIIIIIIIIIII   XG:Z:CSTB,0,1[12M]2[1M1X61M]
NL500104:777:HCM3GAFX5:2:21211:25239:12812      189     chr21 45196325  0  *    *       0       0       CGCGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCGGGGTCTCCGCGCCCAGCGCTGGTGTCGGGAGGGAGCG     !I!!II!!IIIIIIIIIIIIIIIIII!III!IIIII!!III!IIIIIIIIIIIII!IIIIII!IIIIIIIIIIII   XG:Z:CSTB,0,1[12M]2[1M1X23M1X37M]
NL500104:777:HCM3GAFX5:2:11202:2727:9211        189     chr21 45196325  0  *    *       0       0       GCGCGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCTGGGTCTCCGCGCCCAGCGCTGGTGTCGGGAGGGAGC     I!I!IIII!IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII!IIIIIIIIIIIIIIIIIIII!IIIIIIIIIII   XG:Z:CSTB,0,1[1S12M]2[1M1X60M]
NL500104:777:HCM3GAFX5:2:21308:17388:5398       125     chr21 45196325  0  *    *       0       0       GCGCGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCTGGGTCTCCGCGCCCAGCGCTGGTGTCGGGAGGGAGC     I!I!IIII!IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII!IIIIIII!IIIIIII!IIII!IIIIIIIIIII   XG:Z:CSTB,0,1[1S12M]2[1M1X60M]
NL500104:777:HCM3GAFX5:3:21407:19722:5663       125     chr21 45196325  0  *    *       0       0       CGGGGGGCGGGGCGGGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCTGGGTCTCCGCGCCCAGCGCTGGTGT     !I!III!!III!!I!IIII!IIIIIIII!IIIIIIIIIIIIIIIIIIII!III!IIIIIIIIIIIIIIIIIIIII   XG:Z:CSTB,0,1[2M1X9M]1[2M1X9M]2[1M1X49M]
NL500104:777:HCM3GAFX5:1:11102:16995:20161      189     chr21 45196325  0  *    *       0       0       CGCGGGGCGGGGCGCGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCTGGGTCTCCGCGCCCAGCGCTGGTGT     II!IIII!IIIII!!III!!IIIIIIIII!IIIIII!IIIIIIIIIIIIIIIIIIII!III!IIIII!I!IIIII   XG:Z:CSTB,0,1[12M]1[12M]2[1M1X49M]
NL500104:777:HCM3GAFX5:4:21512:6434:14465       125     chr21 45196325  0  *    *       0       0       GCGCGGGGCGGGGCGGGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCTGGGTCTCCGCGCCCAGCGCTGGTG     I!IIIIII!IIII!I!IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII!I!IIIIIIIIIIIIIII!II!I   XG:Z:CSTB,0,1[1S12M]1[2M1X9M]2[1M1X48M]

grep -v "#" results/19A5405.vcf
chr21  45196324 .       G       <STR2>  .       PASS    END=45196360;REF=3;RL=36;RU=CGCGGGGCGGGG;VARID=CSTB;REPID=CSTB  GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC     1/1:SPANNING/SPANNING:2/2:2-2/2-2:112/112:184/184:0/0:55.288681

Hi ,
I am facing an issue during compilation. Could you please help me with the below error?

make[5]: *** [thirdparty/graph-tools/CMakeFiles/graphtools.dir/src/graphalign/GappedAligner.cpp.o] Error 1
make[4]: *** [thirdparty/graph-tools/CMakeFiles/graphtools.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [reviewer-prefix/src/reviewer-stamp/reviewer-build] Error 2
make[1]: *** [CMakeFiles/reviewer.dir/all] Error 2
make: *** [all] Error 2

Thanks and Regards,

ysayyed

Good day,

I would like to get some information about whether it is possible to get the results not only for one locus, but for some of them. If not, is it appropriate to add, for instance, --loci {LocusID1, LocusID2, .. LocusIDN} in the future?

Thanks a lot.

Hi,
I am new with REViewer can I encounter an error with the "BGZF header".
As output i get an empty ".metrics.tsv" and ".phasing.tsv" file and no images.
Do you know a solution for this?

BAM_EXPANSIONHUNTER="patientID_realigned.bam"
samtools sort patientID_realigned.bam -o patientID_realigned.sorted.bam
samtools index patientID_realigned.sorted.bam patientID_realigned.bam.bai

$ REViewer \

--reads $BAM_EXPANSIONHUNTER
--vcf $VCF_EXPANSIONHUNTER
--reference $REFERENCE_GENOME
--catalog $VARIANT_CATALOG
--locus AFF2,AR,ATN1,ATXN1,ATXN10,ATXN2,ATXN3,ATXN7,ATXN7,ATXN8OS,ATXN8OS,C9ORF72,CACNA1A,CBL,CNBP,CSTB,DIP2B,DMPK,FMR1,FXN,GIPC1,GLS,HTT,JPH3,NIPA1,NOP56,NOTCH2NL,PABPN1,PHOX2B,PPP2R2B,RFC1,TBP,TCF4
--output-prefix $OUTPUT_PREFIX
[2022-10-28 13:21:13.966] [info] Loading specification of locus AFF2
[E::bgzf_read_block] Invalid BGZF header at offset 590043
[E::bgzf_read] Read block operation failed with error 2 after 0 of 4 bytes
[2022-10-28 13:21:13.968] [info] Extracted 0 frags
[2022-10-28 13:21:13.968] [info] Calculating fragment length
[2022-10-28 13:21:13.974] [error] There are no read alignments in the target region

I appreciate your help,
/Tine

Hi,
I have couple of questions about interpretation of REViewer graphs.

1- How are base substitutions and deletions displayed in the graphs generated by REViewer?

2- What does this dark line signify?

3- Some graphs have three reads aligned (the one in between are IRRs). How reliable are genotypes supported by such three reads (given that the flanks are 100% matching)?

4- Why are some reads of the same color but lighter in appearance?

Thank you,
Hasna

Hello,

It would be fantastic to have a template with the repeat-size info (every 5 repeats or so).

--1----------------------5--------------------------10---------------------------15---------------------
CGG-CGG-CGG-CGG-CGG-CGG-CGG-CGG-CGG-CGG-CGG-CGG-CGG-CGG-CGG-CGG-CGG-CGG-

It could be nice to show ExpansionHunter CIs in addition to the genotype sizes to make it easier to build intuition about CIs.