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A user rightly [points out](http://gatkforums.broadinstitute.org/gatk/discussion/comment/32631#Comment_32631) that different versions of HaplotypeCaller may produce GVCFs that are not directly compati…
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): 1.1.5
**To Reproduce**
Exact bcbio command you have used:
```
bcbio_nextgen.py ../config/single_test_sample-merged.yaml -t ipy…
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gVCF files represent even non-variant sites as records. We should just ignore all non-variant sites in the input VCF so that the result is identical to the one that one would have gotten had one run t…
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Hello GATK team!
## Bug Report
### Affected tool(s) or class(es)
mutect2
### Affected version(s)
- Latest public release version: 4.2.6.1
### Description
getting fail for all scatt…
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### Need
As a user, I want clear outputs. At the moment variant files are a mix of vcf and bcf, some indexed and some not, some compressed and some not.
### Suggested approach
Standardise output va…
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I'm trialing using GLnexus to merge gVCFs produced by the isaac/starling workflow from Illumina, as an alternative to using gvcfgenotyper (as gvcfgenotyper is extremely memory heavy).
I know it's n…
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comma or tab separated? how about pairwise sequencing?
can I use compressed files, like gz or tar.gz?
here is an example of my manifest.tsv, is this ok?
########################################…
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we're missing this functionality in GATK4, blocked by #2429
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Hi there,
We trying to merge joint Edico-Dragen called gVCFs (one VCF file per family) and noticed two issues:
Error 1: "Invalid: allele is not a DNA sequence" - that seems to happen if an aster…
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Open this issue as an aggregation for optimization suggestions.
- [ ] Alignment #47
- [ ] Marking duplicates, BQSR, sorting
- [ ] Metrics
- [ ] Validate Gvcf