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mutect2 get more variations after add filter parameters

weikangfeiweikangfei chinaMember ✭✭

I run twice based on same data with different parameters, but got strange results.

I will appreciate if can be answered.

Method 1:
gatk-4.1.2.0/gatk Mutect2 -R -I A.bam -I B.bam -tumor A -normal B --af-of-alleles-not-in-resource 0.001 --germline-resource af-only-gnomad.raw.sites.b37.vcf.gz --disable-read-filter MateOnSameContigOrNoMappedMateReadFilter -O somatic.vcf.gz

Method 2:
gatk-4.1.2.0/gatk Mutect2 -R -I A.bam -I B.bam -tumor A -normal B --disable-read-filter MateOnSameContigOrNoMappedMateReadFilter -O somatic.vcf.gz

Method 1 got more variation results than Method 2.

I checked the additional variation in af-only-gnomad.raw.sites.b37.vcf.gz

2 92325922 . A T 5070.26 PASS AC=9;AF=2.241E-4
2 92325930 . C G,T 12932.37 PASS AC=40,20;AF=0.001018,5.089E-4
2 92325953 . A C,G 130428.94 PASS AC=75,790;AF=0.001952,0.021
10 38877202 . CAAAT TAAAT,*,CGAAAT 322492.27 PASS AC=791,5,1;AF=0.022,1.364E-4,2.727E-5
10 38877212 . GGAATGGAATCTTCGAATGGAATCATCATTGAATGGAATTGAATGGAATCATCGAATGGAATAGAATGGAATAATC *,GGAATGGAATCATCATTGAATGGAATTGAATGGAATCATCGAATGGAATAGAATGGAATAATC106413.61 PASS AC=7,1;AF=4.126E-4,5.895E-5
11 51582780 rs6598131 T A 3305822.21 PASS AC=3759;AF=0.093
12 124543689 . C CT 366.08 PASS AC=22;AF=5.416E-4
12 124543700 . C T 1351.74 PASS AC=24;AF=5.908E-4
22 48730294 . G A 758.09 PASS AC=3;AF=7.386E-5

I can't understand what happened and hope for explanation.

Best wishes,
Kangfei

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Best Answer

Answers

  • weikangfeiweikangfei chinaMember ✭✭

    Hi @bhanuGandham
    Yes, methods 1 got more variants and I checked them in germline-resource af-only-gnomad.raw.sites.b37.vcf.gz, it showed that part of them were in it . Among them , "11 51582780 rs6598131 T A 3305822.21 PASS AC=3759;AF=0.093" was dbsnp~

    I don't know why this happened.

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @weikangfei

    Try to run it without the --af-of-alleles-not-in-resource argument. Starting with v4.0.4.0, GATK recommends the default setting of --af-of-alleles-not-in-resource, which the tool dynamically adjusts for different modes.
    Let me know if the issue persists.

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