Comments (9)
Hello!
-For the vcfm2acf, I am not sure how one should interpret "0/0/0/0/0/0/0/0" in terms of genotype. Is this a polyploid genome? I am not familiar with that genotyper, not to be dogmatic, I would tend to stick with published methods at least for testing.
- Is there a fai file? Could you stick the fai file somewhere and maybe a bit of the bam file?
from glactools.
@yzongzjnu have you any update regarding this?
from glactools.
is this fine? can I close the issue?
from glactools.
Hi, I'm having pretty much the same issue - I'm happy to open a new issue if you prefer.
My command:
glactools vcfm2acf --fai reference.fasta.fai biallelic.snps.vcf.gz > biallelic.snps.acf
and the error:
SimpleVCF: unable to determine genotype for field=#.# at position: 1:33
Error: GlacParser tried to read 4 bytes but got 0
My VCF was generated with Freebayes, filtered with BCFtools and pruned for linkage with PLINK.
Any suggestions you have would be greatly appreciated.
Cheers
from glactools.
from glactools.
Thank you for responding. Here's the line:
1 33 1_33 C T 131342 PASS AB=0.484013;ABP=9.05068;AC=783;AF=0.628606;AN=1298;AO=6505;CIGAR=1X;DP=13284;DPB=13284;DPRA=0.819753;EPP=2317.25;EPPR=72.2722;GTI=117;LEN=1;MEANALT=1;MQM=41.5646;MQMR=33.472;NS=853;NUMALT=1;ODDS=0.00103555;PAIRED=0.79339;PAIREDR=0.528101;PAO=0;PQA=0;PQR=0;PRO=0;QA=236494;QR=189135;RO=6779;RPL=243;RPP=12096.6;RPPR=3587.12;RPR=6262;RUN=1;SAF=4714;SAP=2855.11;SAR=1791;SRF=3494;SRP=17.0023;SRR=3285;TYPE=snp;technology.illumina=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:1:0,1:0:0:1:38:-3.79727,-0.30103,0 1/1:11:0,11:0:0:11:362:-32.645,-3.31133,0 1/1:7:1,6:1:16:6:186:-15.4907,-0.557485,0
from glactools.
from glactools.
from glactools.
Seems to be working now, thank you Gabriel! Much appreciated.
from glactools.
Related Issues (20)
- Need more details about program usepopsrootanc HOT 4
- cannot determine the root allele
- install error HOT 1
- compile errors HOT 4
- run error about Cannot write to /dev/stdout. HOT 16
- Can not use bed track with glactools bam2acf HOT 1
- SQ fields differ in the header HOT 1
- plink(bed-bim-fam) to treemix HOT 5
- vcf to G-phocs HOT 1
- problems about vcfm2acf HOT 2
- bam2acf for multiple samples HOT 1
- vcf to GROSS convertion HOT 2
- install issue HOT 2
- epo file format HOT 27
- vcfm2acf issue HOT 7
- installation trouble HOT 4
- --onlyGT confusion HOT 1
- Error in vcfm2acf HOT 9
- vcfm2acf deal for vcf file HOT 15
- issue with setting root 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 glactools.