How do I merge f1r2.tar.gz files when parallelizing Mutect2 pipeline?

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Jenifer

• October 28, 2020 17:25
• Edited

Hi!

I am running the following snakemake command line using GATK 4.1.7.0 version:

"gatk Mutect2 -L $chr -R {reference} --tumor-sample {tumour_name} --normal-sample {normal_name} --input {tumour_bam} --input {normal_bam} -germline-resource {germline_resource} -pon {pon} --f1r2-tar-gz $outputf1r2 --output $outputvcf;"

 

As I am running this command for each chromosome, I am having 25 different {chr}.f1r2.tar.gz files. This also happens for the vcf and the stats files, but I found gatk gathervcf and gatk mergestats functions to solve this issue. How can I merge f1r2.tar.gz files?

Thanks

 

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  Genevieve Brandt (she/her)

  • October 30, 2020 17:33

  Jenifer This has been discussed previously on the forum: https://gatk.broadinstitute.org/hc/en-us/community/posts/360060460131-GATK4-Parallelizing-genotypegvcfs

  If you have questions about GATK and Mutect2, check out our webinar event happening on November 17th! We encourage you to post your questions and topic requests before the event so we can answer as many questions as possible during the event. There is a new topic on the forum just for the Webinar, hope you join in!

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