Comments (6)
Are you saying you've swapped hg19.fa.gz for our hs37d5.fa.gz fasta? That won't work because the chromosome names are different - 20 in hs37d5 and it sounds like chr20 in hg19.fa.gz. DeepVariant requires the BAM file and the reference genome to have consistent contigs.
from deepvariant.
I do not think this is the case. The example BAM file, NA12878_S1.chr20.10_10p1mb.bam, contains reads mapped to chromosome 20 which show chr20 in RNAME for all the reads. This means the fasta file should contain chromosomes named as 'chr'.
Morever, the example fasta, ucsc.hg19.chr20.unittest.fasta, comes from hg19 and it works. Any idea why using the entire genome would make the run fail?
from deepvariant.
The only real requirement is that the fasta and the BAM need to have a large number of consistent contigs (meaning same length in bp and with the same name) and DeepVariant will process the dataset. If you do samtools view -H on the BAM and cat the hg19.fa.gz.fai file, do these have the same set of contigs with the same lengths?
from deepvariant.
Ok, might be doing something wrong. How do you create your .gz.fai file? Is it coming from indexing a fasta file compressed with bgzip or how?
from deepvariant.
I already have a copy of hs37d5.fa on my machine, so to create a gzipped, indexed version I do:
cp hs37d5.fa /tmp
bgzip /tmp/hs37d5.fa
samtools faidx /tmp/hs37d5.fa.gz
head /tmp/hs37d5.fa.gz.fai
1 249250621 52 60 61
2 243199373 253404903 60 61
3 198022430 500657651 60 61
4 191154276 701980507 60 61
5 180915260 896320740 60 61
6 171115067 1080251307 60 61
7 159138663 1254218344 60 61
8 146364022 1416009371 60 61
9 141213431 1564812846 60 61
10 135534747 1708379889 60 61
from deepvariant.
Ok, I think that solves the issue. When indexing over the gz only indexed the first chromosome for some reason in my machine
from deepvariant.
Related Issues (20)
- Errors on testing DeepTrio on PacBio samples HOT 4
- Error on testing deepvariant for WES HOT 5
- splitting bam for deepvariant input HOT 5
- /opt/deepvariant/bin/deeptrio/run_deeptrio: No such file or directory HOT 6
- Issue with running docker image HOT 8
- I have built Deepvariant:1.6.0 successfully in my Ubuntu20.04. I want to know something about its usage. HOT 4
- Using PAR region flag seems to log NativeBedReader endlessly HOT 5
- Checkpointing / resuming analysis HOT 4
- How to understand the running results of deepvariant? HOT 3
- Representation of hemizygous genotypes as homozygous when using --haploid_contigs in postprocess_variants HOT 2
- Unable to run DeepVariant with Star Alignments for RNASeq data HOT 2
- docker pull from google/deepvariant:1.6.0-gpu ,but the python version is 3.11 and the proto file cannot import HOT 2
- deepvariant error on gpu HOT 2
- Updates to underlying tools in docker HOT 2
- Debug source code, but bazel compilation has some problems HOT 10
- Error running DeepVariant v1.1.0 HOT 4
- stuck for hours at candidate finding HOT 2
- GPU with less than 16GB memory HOT 3
- Is there any option to use sequencing error correction part only?
- deepvariant 1.6.0 with singularity gpu support HOT 5
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from deepvariant.