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@mbabadi commented on [Wed May 24 2017](https://github.com/broadinstitute/gatk-protected/issues/1097)
Devin McCabe discovered a _bug_ (read: bad model behavior) in TargetCoverageSexGenotyper. The bug…
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Hello,
The DELLY VCFs write per-sample genotypes roughly like the following for no-call samples:
./.:.,.,.:0:LowQual:0:0:0:-1:0:0:0:0
note the ".,.,." for genotype likelihoods. GATK chokes on this…
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Hi,
I ran into the following error when combining gVCF files generated by the HaplotypeCaller:
> htsjdk.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: Discordant f…
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Thank you for this well done tool.
Is it possible to genotype on a restricted sample list from previously built chunks? This would enable one to re-use previously built chunks for cohort VCFs, rath…
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Hello,@rhshah,sorry for bother you again,when i run iCallSV,i met a error like below:
command:
R --slave --vanilla --args 5 /gpfs/users/yanghao/project/shi-jian-zhi-ping/t_n_20171030/illumina /gpf…
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Hi,
A (wrong?) behaviour with bcftools merge when dealing with either ref or missing genotypes such as the below example:
File 1 extract:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT V00055 …
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Hello,
I am trying to use your library to load and read VCF file, my code is:
```
import vcf
vcf_reader = vcf.Reader(open('6788.vcf', 'r'))
record = next(vcf_reader)
```
I tried Py2.7 …
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I encountered a weird issue that I wanted to check with you regarding this site: http://gnomad.broadinstitute.org/variant/7-74306893-A-G
This site is reported as multiallelic (A/G and A/T) on the w…
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Hello!
Thanks for the excellent pipeline.
In 1.0.7 gemini load command fails (unnecessary details omitted):
```
[2018-01-17T22:43Z] gemini load --passonly --skip-gerp-bp -v work/gemini/1031…