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Hi,
I am writing to seek your assistance with an issue I have encountered while using the iWhale pipeline. It is a highly efficient tool, and I appreciate its capability to manage reanalysis seamless…
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Hello,
I'm testing gatk4.3 against 3 WES samples. For less time comsuption, I scattered the bed file into 45 small interval list. But an error prompted out in the GermlineCNVCaller step with the er…
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### Description of feature
https://gatk.broadinstitute.org/hc/en-us/articles/360036510892-VariantRecalibrator
https://gatk.broadinstitute.org/hc/en-us/articles/360037056912-ApplyVQSR
=> Also look…
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Hi,
I'm trying to use GLnexus v.1.2.6 to merge g.vcf files generated by the GATK HaplotypeCaller, using the gatk configuration pre-set. For my project, I'm merging WGS calls from ~300 individuals seq…
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**Is your feature request related to a problem? Please describe.**
Yes, the combinegvcfs tool fails to allocate or process large sample sizes.
**Describe the solution you'd like**
A solution is t…
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Hello,
I am running bcbio-nextgen-vm on sample data and I have experienced problem with gatk-framework even it is already installed. Any suggestion please ?
[2018-10-28T02:05Z] 2018-10-28 02:05:…
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### Description of the bug
Hi,
I'm trying to run sarek with "mutect2" for variant calling.
Pipeline completes successfully, but the folder "output/variant_calling/" is empty.
It seems like proce…
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1. We need a script to take snapshots of the [GATK total downloads page](https://somsubhra.com/github-release-stats/?username=broadinstitute&repository=gatk) every month and report the number of times…
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Greetings,
I have installed baga and everythin has worked well until I get to the indel realignment step where it need GATK to do it.
I have got GATK version 3.6-0-g89b7209 which works on java 1.8.
>…