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Mutect2 vcf FORMAT field

andeveandeve MilanoMember

Hi,
I’m trying to use Mutect2 (GATK version 3.7) for somatic mutation calling.
I noticed that if I use it with the default parameters in the FORMAT field I have the following informations:
GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1
If I add the annotation modules, for example -A FisherStrand and -A StrandOddsRatio, the FORMAT field contain only GT:AD:AF.
Why?

This is my command line:
java -jar GenomeAnalysisTK.jar -T MuTect2 \
-R reference.fasta \
-I:tumor tumor.bam \
-I:normal normal.bam \
--dbsnp dbsnp_138.hg19.vcf \
--cosmic hg19_cosmic_v54_120711.vcf \
-o output.vcf \
-L targets.interval_list \
-A FisherStrand \
-A StrandOddsRatio \

Thank you very much!

Andrea

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Comments

  • SheilaSheila Broad InstituteMember, Broadie admin

    @andeve
    Hi Andrea,

    That may be a bug, but it is not likely to get fixed because GATK4 MuTect2 is now out and available for testing. It also features a new strand bias annotation. You can test it out here.

    -Sheila

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