Can I create Mutet2 PON with hg38 instead of hg19?
Dear Terra,
is there any PON/Mutect workflow that uses the hg38 human genome reference other than hg19 required by these gatk workflows?
https://app.terra.bio/#workspaces/help-gatk/Somatic-SNVs-Indels-GATK4
https://portal.firecloud.org/?return=terra#methods/gatk/mutect2_pon/8
My analysis_ready_bam were aligned with hg38 and I was wondering if running panel of normals with hg19 (aka b37) will have any significant impact on other downstream analysis?
Thanks
sam
Comments
1 comment
Yes, you'll just need to change the workflow attribute configurations to hg38 reference data. You can find hg38 equivalent reference files for mutect2 here: https://console.cloud.google.com/storage/browser/gatk-best-practices/somatic-hg38/
Side note you should use the latest version of the workflow which can be found in the Somatic-SNVs-Indels-GATK4 featured workspace.
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