Dear GATK Team,
Thank you for the informative Mutect2 webinar.
Please could you clarify whether an interval list (e.g. interval.list or interval.bed) used in other GATK tools (e.g. Mutect2) to cover specific genomic intervals is suitable to use with the --intervals (-L) option for GetPileupSummaries in the Somatic short variant discovery (SNVs + Indels) workflow?
If not, can it be transformed into a common-biallelic.vcf or would it be recommended to just use the same common-biallelic.vcf as in the --variant (-V) option?
Thank you for your time and help.
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