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dbIndel as input for Mutect2

escaonescaon Limoges, FranceMember

Hello,

I was wondering if Mutect2 accepts a "dbIndel" as input.
Something similar to the "--dbsnp" argument, but for known Indels.

I am currently using GATK bundle hg38 files in my Mutect2 pipeline :
dbsnp_146.hg38.vcf.gz is my "--dbsnp" argument
Could Mills_and_1000G_gold_standard.indels.hg38.vcf.gz be used as an argument value somewhere ?

Best regards

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  • escaonescaon Limoges, FranceMember

    Ok,

    Then, shall i merge dbsnp_146.hg38.vcf & Mills_and_1000G_gold_standard.indels.hg38.vcf into a single vcf file ?
    OR
    Give 2 --dbsnp arguments in the same command : --dbsnp dbsnp_146.hg38.vcf --dbsnp Mills_and_1000G_gold_standard.indels.hg38.vcf ?

    Thanks for your reply

  • escaonescaon Limoges, FranceMember

    Hum, i may have been reading this wrong :

    Are you are saying that indels in the Mills_and_1000G_gold_standard.indels.hg38.vcf are included in the dbsnp_146.hg38.vcf ?

    Is the "matter of historical legacy" referring to the --dbsnp argument or the name of the dbsnp.vcf file ?

    Sorry if these are trivial questions

  • escaonescaon Limoges, FranceMember

    Ok thx a lot,

    I'll stick to using --dbsnp dbsnp_146.hg38.vcf then (since it does take indels into account too)

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