gatk

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## Bug Report ### Affected tool(s) or class(es) FilterAlignmentArtifacts supplied: Variant File, BAM File, Genome, (hg19) --bwa-mem-index-image (from resource bundle (hg38) ### Affected version(s) - [x ] Latest public release...

dansteiert

Homebrew

2

Hi is it possible to have a hombrew formula ? thanks

BenjaminDEMAILLE

Problem in gvcf interplay between clair3 and gatk

1

I realized an issue, when feeding clar3 gvcf files into GenotypeGVCFs of GATK for cohort calling. The SNP where it became obvious is a SNP likely located on one copy...

johannesgeibel

VariantAnnotator giving error "No overlapping contigs found"

1

## Bug Report ### Affected tool(s) or class(es) VariantAnnotator ### Affected version(s) GATK-4.6.1.0 ### Description I am having problem running the VariantAnnotator. I am assuming that the command can run...

khanshahan

Reference isn't being parsed/detected correctly when using CalibrateDragstrModel in parallel mode

8

### Instructions The github issue tracker is for bug reports, feature requests, and API documentation requests. General questions about how to use the GATK, how to interpret the output, etc....

nvnieuwk

### Instructions The github issue tracker is for bug reports, feature requests, and API documentation requests. General questions about how to use the GATK, how to interpret the output, etc....

SiddhiJani

Please add java to the yaml file distributed through GitHub for conda installation (e.g. openjdk=17). It is after all a dependency of gatk... Really, that should go for samtools, bedtools,...

stuartwillis

python exited with 1. Theano error.

1

## Bug Report ### Affected tool(s) or class(es) GATK-gCNV-GermlineCaller ### Affected version(s) 4.3.0.0 ### Description ` 00:16:50.019 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gpfs/hpc/home/lijc/xiangxud/software/miniconda3/envs/gatk4/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 00:16:50.035 DEBUG NativeLibraryLoader - Extracting libgkl_compression.so...

lovelycatZ

GATK 4.6. SelectVariants not applying --select filters

1

## Bug Report ### Affected tool(s) or class(es) gatk SelectVariants ### Affected version(s) gatk 4.6.0. (not tested on 4.6.1.) ### Description select statements are ignored. When using the following filter...

FLsandell

Could not load genomicsdb native library

12

With GATKv4.0.0.0, when I try to run GenomicsDBimport, it crashes and gives this error message: > 19:29:01.249 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/gatk/4.0.0.0/gatk-package-4.0.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 19:29:01.391 INFO GenomicsDBImport - ------------------------------------------------------------ 19:29:01.391...

owensgl