Install GATK 3.8 with conda

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2.2 years ago

Filago ▴ 100

Dear all, I want to install GATK 3.8 with conda from the following link: https://anaconda.org/bioconda/gatk

However, after installation the version seems to be 3.6... Does somebody know how to get v 3.8?

Furthermore, after registering the file downloaded from here:

https://console.cloud.google.com/storage/browser/gatk-software/package-archive/gatk;tab=objects?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&prefix=&forceOnObjectsSortingFiltering=false

I am not able to run a command like e.g. HaplotypeCaller:

##### ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: HaplotypeCaller

Does anyone know whats going on here?

Best, Andreas

GS GATK • 1.3k views

ADD COMMENT • link updated 2.2 years ago by Ram 44k • written 2.2 years ago by Filago ▴ 100

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How are you running HaplotypeCaller?

ADD REPLY • link 2.2 years ago by Ram 44k

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gatk -T HaplotypeCaller -R GCF_000001405.25_GRCh37.p13_genomic.fna.gz -I wgEncodeUwRepliSeqBg02esG1bAlnRep1.bam -O test.g.vcf -ERC GVCF

ADD REPLY • link updated 2.2 years ago by Ram 44k • written 2.2 years ago by Filago ▴ 100

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Are you sure you installed GATK 3.8? Your post is awfully deficient on exact commands. What are your conda commands and the command to check on installed version of GATK?

ADD REPLY • link 2.2 years ago by Ram 44k

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