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Install GATK 3.8 with conda

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
• 1,949 views • link
updated by Ram Ram • written by Filago • Filago

How are you running HaplotypeCaller?

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written by Ram Ram 
gatk -T HaplotypeCaller -R GCF_000001405.25_GRCh37.p13_genomic.fna.gz -I wgEncodeUwRepliSeqBg02esG1bAlnRep1.bam -O test.g.vcf -ERC GVCF
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updated by Ram Ram • written by Filago • Filago

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?

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written by Ram Ram

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