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when I use gatk to identify variants in a bam file converted from gam using vg surject, I get error

7

@jmarshall when i use [(vg surject)](https://github.com/vgteam/vg) convert gam to bam, then use gatk detect variants, it report error as bleow  the genome no chromosome is longer than 512M，i can't...

ChenDepp

Hi https://gatk.broadinstitute.org/hc/en-us/community/posts/34245458141083-VariantFiltration-isAvailable-and-isNoCall-expressions-for-genotype-filtration-work-unexpectedly Only isHom, isHet type entries work however isAvailable, isNoCall etc. are not working at all. This could well be a HTSJDK bug but I am not sure. VariantFiltration...

gokalpcelik

GtfToBed errors out with `because "gene" is null`

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This bug report is regarding a new tool, GtfToBed, which was introduced in #8942 PR. The following code creates a reproducible example of the error: ## Get the necessary files...

mmahmoudian

Efficiently perform simple merge/append on many VCFs?

4

Hello, This isnt exactly a GATK question, but I think this problem would be faced by many GATK users. Our current practice is to run many GATK-based jobs scatter/gathered, meaning...

bbimber

Docker 4.6.1.0 image not finding includes

1

First, thank you all for your hard work. I would like to submit a bug in the latest docker image. I use the gatk docker image as a base for...

pjgreer

Miscalling of SNPs and GQ value of 0

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## Problem report ### Affected tool(s) or class(es) HaplotypeCaller ### Affected version : 4.1 ### Description We used gatk HaplotypeCaller to find SNPs in our samples, following this command line:...

Sgornard

negative CNN_1D scores

2

Hello, I used the Sarek pipeline to detect germline variants ( working with 30X WGS). After variant calling with haplotypecaller, the pipeline runs CNNScoreVariants and FilterVariantTranches. However, the number of...

MarionFresquet

macOS install

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Hi ! How can install on macOS with python3. After install it's still looking for python instead of python3 ``` benjamin@MacBook-Pro-de-Benjamin ~ % /opt/homebrew/bin/gatk/build/resources/main/gatk env: python: No such file or...

BenjaminDEMAILLE

[DO NOT MERGE]

13

Testing updates to the GATK conda environment in support of future conda tools.

jamesemery

Fixing what looks like a a bug in MendelianViolationEvaluator

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* there was a duplicated condition which looks like a typo and causes nNoCall to be undercounted @bbimber `mv.getFamilyCalledCount` was used twice as the condition in this if statement, I'm...

lbergelson