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Proposed output of GL string batch processing:
Column names; description
Sample ID; self-explanatory
nA; number of alleles in HLA-A ambiguity string (sum over both haplotypes)
nB, nC, nDRB1, etc.
nC…
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@vruano commented on [Wed May 18 2016](https://github.com/broadinstitute/gsa-unstable/issues/1376)
## Bug Report
### Affected tool(s)
All tools that use AFCalculators (HC, GenotypeGVCFs etc).
### Af…
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@LeeTL1220 commented on [Mon May 23 2016](https://github.com/broadinstitute/gatk-protected/issues/524)
- [ ] File issues for evaluations (and make sure each evaluation is described, including ground …
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Hi,
I am trying to convert adam to vcf . But getting this error. Is there any other way I can convert the adam file to .vcf file?
Command:
./adam-submit transformVariants hdfs://ip-10-48-3-5.…
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Devin McCabe discovered a _bug_ (read: bad model behavior) in TargetCoverageSexGenotyper. The bug was discovered by feeding the tool with coverage data on autosomes + X chromosome (no Y chromosome). S…
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_From @jbloom22 on September 1, 2015 18:20_
Kaitlin has written a python tool that can serve as model. From Kaitlin:
The most recent version is attached (3.93). The biggest issue that I've yet to r…
cseed updated
7 years ago
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Hi there,
using WASP/snp2h5 I have just encountered the folowing error which I don't seem to be able to make sense of:
```
[mce@dzne-go-cn03 test]$ /home/mce/WASP/snp2h5/snp2h5 --chrom /home/mc…
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In a joint calling run with 11,000 samples, and broken up into over 10,000 scatters, a single one failed with a NPE. I was able to get around it for now by just ignoring that scatter for the output, …
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The definition of err_mod_t has been commented out in recent releases. Because of this I cannot built angsd versions later than 0.910.
I've already tried using HTSlib 1.3.2 to see if this would solve …
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Hello Adam,
I am trying to use the new version of create_consensus.sh and I am getting this error:
`amorales@dacelo:/disks/dacelo/data/analyses/RB7_data_analysis/merged_bams_alignment_3$ bash …