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Mutect2 --artifact_detection_mode

I have a question how to create Panel of Normals (PON) using Mutect2: do we still need to add the dbSNP and Cosmic parameters when running the following command for each normal BAM in artifact_detection_mode? Will command lines with/without dbSNP and cosmic affect the PON VCF calling?
"java -jar GenomeAnalysisTK.jar \
-T MuTect2 \
-R reference.fasta \
-I:tumor normal1.bam \
[--dbsnp dbSNP.vcf] \
[--cosmic COSMIC.vcf] \
--artifact_detection_mode \
[-L targets.interval_list] \
-o output.normal1.vcf"

Thanks,

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Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @wmy
    Hi,

    For GATK3, you can to input the Cosmic and dbSNP files. Have a look at the documentation. However, I don't think the Cosmic file does anything. The dbSNP file is use to annotate the rsid columns. Have a look at the GATK3 MuTect2 tutorial here.

    -Sheila

  • wmywmy MarylandMember
    edited September 2017

    Thanks, Sheila!
    So, does that mean the variants and variant counts in the output.normal1.vcf from above command line will be exact same with/without dbSNP file? Is the only difference the annotation information in the rsid column after using the dbSNP file? Will that rsid annotation information affect CombineVariants step when generate the final PON?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @wmy
    Hi,

    Yes, I think the dbSNP file does not affect which variants are output, just the rsid column.

    The rsid information should not affect the PoN creation.

    -Sheila

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