GetPileupSummaries following Mutect2: what inputs are suitable for --intervals (-L)?

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ISmolicz

• November 17, 2020 15:53

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.

Kind regards.

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  Brian Haas

  • November 17, 2020 16:02

  Hi,

  Good question.  If you're using whole exome data and have an intervals file, I think you should use that for the -L parameter, but use the common variants vcf for the -V option.

  If you're doing whole genome sequencing, then using the same parameter for -L and -V is likely most appropriate.

  (Other GATK folks, please correct me if that's wrong... )

   

   

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  ISmolicz

  • November 17, 2020 16:24

  Thank you for confirming Brian Haas - much appreciated. I imagine that for targeted sequencing panels the intervals file can be used for the -L parameter also, if it can be for whole exome data.

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