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how can I get germline-resource file for Mutect 2

Hi team,
I am running Mutect 2 on mouse data, may I ask how can I get these two files for my data?
1. the input .vcf file for --germline-resource (eg. resources/chr17_af-only-gnomad_grch38.vcf.gz)
2. the input .vcf file for GetPileupSummaries -V (eg. resources/chr17_small_exac_common_3_grch38.vcf.gz)

Thanks for any of your kind help!

Answers

  • Thanks for your kind help @manba , but my data is mouse data, I think the google cloud only has the human vcf file
  • bshifawbshifaw moonMember, Broadie, Moderator admin

    Hi Claire,

    I'm checking up on this now.

  • bshifawbshifaw moonMember, Broadie, Moderator admin

    @claire1011

    We don't provide non-human resource bundles, you will have to find or create equivalent mouse resource files.
    You may find the Mutect2 tutorial useful, it describes a bit of the resources you mentioned above.
    --germline-resource : "Annotate variant alleles by specifying a population germline resource with --germline-resource. The germline resource must contain allele-specific frequencies, i.e. it must contain the AF annotation in the INFO field [4]. The tool annotates variant alleles with the population allele frequencies. "
    GetPileupSummaries -V : "Use a population germline resource containing only common biallelic variants, e.g. subset by using SelectVariants --restrict-alleles-to BIALLELIC, as well as population AF allele frequencies in the INFO field. The tool tabulates read counts that support reference, alternate and other alleles for the sites in the resource."

  • MT_badrMT_badr Member
    > @claire1011 said:
    > Hi team,
    > I am running Mutect 2 on mouse data, may I ask how can I get these two files for my data?
    > 1. the input .vcf file for --germline-resource (eg. resources/chr17_af-only-gnomad_grch38.vcf.gz)
    > 2. the input .vcf file for GetPileupSummaries -V (eg. resources/chr17_small_exac_common_3_grch38.vcf.gz)
    >
    > Thanks for any of your kind help!

    Hi Claire, i am facing the same problem with my mouse data right now, did you manage to find any useful germline resource with AF for mice to be used with Mutec2 ?
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