Tia

we are using MuTect2 to call somatic SNVs and indels (gatk v 4.1.2.0). we find error in F1R2 plus F2R1 not equal AD. The follow is our command: gatk Mutect2 -R /home/MuTect2/genome/hg19.fa \ -I /home/MuTect2/DATA/01_BQSR/ECT37.sorted.dedup.recal.bam \ -I /home/MuTect2/DATA/01_BQSR/EPT37.sorted.dedup.recal.bam \ -normal ECT37 \ --germline-resource /home/MuTect2/group_37_result/0_known_sites/af-only-gnomad.raw.sites.hg19.vcf \ --panel-of-normals /home/MuTect2/DATA/02_Mutect/PON/PON1/37.pon1.vcf.gz \ --f1r2-tar-gz EPT37_ECT37.f1r2.tar.gz \ --disable-read-filter MateOnSameContigOrNoMappedMateReadFilter \ --bam-output EPT37_ECT37.bam \ -O Pon1.EPT37.N-ECT37.T.unfilter.somatic.vcf and the Mutect2 vcf is GT:AD:AF:DP:F1R2:F2R1:SB 0/0:351,4:0.013:355:184,1:166,3:271,80,4,0 0/1:298,8:0.028:306:154,3:141,5:219,79,8,0 ref_AD=351 alt_AD=4 ref_F1R2=184;ref_F2R1=166 alt_F1R2=1,alt_F2R1=3 ref_ F1R2 + ref_F2R1=350 ,not equal ref_AD (351)

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  • we are using MuTect2 to call somatic SNVs and indels (gatk v 4.1.2.0). we find error in F1R2 plus F2R1 not equal AD. The follow is our command:
    gatk Mutect2 -R /home/MuTect2/genome/hg19.fa \
    -I /home/MuTect2/DATA/01_BQSR/ECT37.sorted.dedup.recal.bam \
    -I /home/MuTect2/DATA/01_BQSR/EPT37.sorted.dedup.recal.bam \
    -normal ECT37 \
    --germline-resource /home/MuTect2/group_37_result/0_known_sites/af-only-gnomad.raw.sites.hg19.vcf \
    --panel-of-normals /home/MuTect2/DATA/02_Mutect/PON/PON1/37.pon1.vcf.gz \
    --f1r2-tar-gz EPT37_ECT37.f1r2.tar.gz \
    --disable-read-filter MateOnSameContigOrNoMappedMateReadFilter \
    --bam-output EPT37_ECT37.bam \
    -O Pon1.EPT37.N-ECT37.T.unfilter.somatic.vcf

    and the Mutect2 vcf is
    GT:AD:AF:DP:F1R2:F2R1:SB 0/0:351,4:0.013:355:184,1:166,3:271,80,4,0 0/1:298,8:0.028:306:154,3:141,5:219,79,8,0

    ref_AD=351
    alt_AD=4

    ref_F1R2=184;ref_F2R1=166
    alt_F1R2=1,alt_F2R1=3
    ref_ F1R2 + ref_F2R1=350 ,not equal ref_AD (351)
    August 1