gatk

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GetPileupSummaries Permanently Stalled but High CPU Usage

5

CPU usage was high. ``` %CPU WallTime Time Lim RSS mem memlim cpus hugemem-ex 105958574 R ds6924 hm82 getpileu 99 07:23:01 16:00:00 1120GB 1120GB 1400GB 37 ``` However, it never...

DarioS

In some cases it may be useful to know what reads are giving rise to which specific variants. I have run into several cases while debugging some strange results where...

odcambc

Serious Security Vulnerabilities in GATK

19

I am looking at using GATK and first checked at the docker image using **_docker pull broadinstitute/gatk_** this container image has 1460 vulnerabilities and a lot of them are critical....

mohitmathew

Implement our version of deTiN

2

Implement whatever model comes out of #3087.

davidbenjamin

* update setup-gcloud@v0 -> v2 since v0 is deprecated

lbergelson

Hi, When I try to run Funcotator, using the below command: gatk Funcotator \ --variant /rsrch5/home/tdccct/ppshah/shared/CAS_MOSAIC/mutect/mrn_2507919/WES/KShaw-ROPR0004-DNA-229761-WX01-T_HMCKJDSX2-4-ATTGGCTC/KShaw-ROPR0004-DNA-229761-WX01-T_HMCKJDSX2-4-ATTGGCTC_filtered.vcf.gz \ --reference /rsrch5/home/tdccct/ppshah/shared/gencode/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta \ --ref-version hg38 \ --data-sources-path /rsrch5/home/tdccct/ppshah/shared/pipelines/mutect/funcotator_dataSources.v1.7.20200521s \ --output /rsrch5/home/tdccct/ppshah/shared/CAS_MOSAIC/mutect/mrn_2507919/WES/KShaw-ROPR0004-DNA-229761-WX01-T_HMCKJDSX2-4-ATTGGCTC/KShaw-ROPR0004-DNA-229761-WX01-T_HMCKJDSX2-4-ATTGGCTC_funcotated.vcf \ --output-file-format...

parth2608

## Bug Report ### Affected tool(s) or class(es) gatk HaplotypeCaller _--do-not-run-physical-phasing false_ ### Affected version(s) gatk-4.4.0.0 ### Description I used **gatk HaplotypeCaller** with parameter _--do-not-run-physical-phasing false_, some missing genotypes were...

Sherry520

LearnReadOrientationModel loads tables for one ref context at a time, reducing memory demands 32x

1

Closes #7948

davidbenjamin

## Bug Report ### Affected tool(s) or class(es) In the tutorial "[(How to part I) Sensitively detect copy ratio alterations and allelic segments](https://gatk.broadinstitute.org/hc/en-us/articles/360035531092)", users are asked to install R components...

eholdmore

Hi, I use funcotator to call somatic mutations as below: ``` gatk Funcotator \ -R $ref/Homo_sapiens_assembly38.fasta \ -V ../${array[1]}.filter.vcf \ -O ${array[1]}.maf \ --output-file-format MAF \ --data-sources-path Funcotator_data/funcotator_dataSources.v1.7.20200521s/ \ --ref-version...

lh12565