Install GATK 3.8 with conda
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18 months 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 • 1.0k views
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How are you running HaplotypeCaller?

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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
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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?

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