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Metochontrial WDL flow allele fraction(AF) is inconcistent with AD?

ahdaahda ChinaMember
edited December 2019 in Ask the GATK team

I had some metochontrial samples, and do GATK meto flow as GATK WDL.
then I find the allele fraction of AF is inconcistent with real alt_fraction,that is AD[2]/DP:
for example,AF of this record is 8.597*10^-4, but real alt_fraction is 78/36748~~0.002,which should be not filtered by low_allele_frac.
chrM 149 . T C . low_allele_frac CONTQ=15;DP=37739;ECNT=29;MBQ=20,20;MFRL=189,190;MMQ=60,60;MPOS=28;OCM=0;POPAF=2.40;SEQQ=93;STRANDQ=2;TLOD=12.96 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:36670,78:8.597e-04:36748:16938,37:19352,39:21680,14990,47,31
then I check other records in the VCF, then I find their AFs are always inconcistent with AD/DP,like below:
this is visible format:

this is real vcf record of above:
chrM 1 . G C . contamination;strand_bias CONTQ=2;DP=15294;ECNT=29;MBQ=20,20;MFRL=169,157;MMQ=60,60;MPOS=12;OCM=0;POPAF=2.40;SEQQ=93;STRANDQ=1;TLOD=26.51 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:15268,26:1.611e-03:15294:7295,11:7350,11:0|1:8568_T_C:8568:10035,5233,18,8 chrM 7 . A G . contamination;strand_bias CONTQ=1;DP=16204;ECNT=29;MBQ=20,20;MFRL=169,157;MMQ=60,60;MPOS=5;OCM=0;POPAF=2.40;SEQQ=93;STRANDQ=1;TLOD=25.52 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:15848,26:1.541e-03:15874:7166,13:7088,13:0|1:8568_T_C:8568:10437,5411,18,8 chrM 14 . T C . strand_bias CONTQ=29;DP=3333;ECNT=24;MBQ=20,29;MFRL=158,194;MMQ=60,60;MPOS=9;OCM=0;POPAF=2.40;SEQQ=52;STRANDQ=1;TLOD=5.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:2939,12:3.283e-03:2951:1467,3:1438,9:1844,1095,5,7 chrM 16 . A G . strand_bias CONTQ=3;DP=3716;ECNT=24;MBQ=20,37;MFRL=159,245;MMQ=60,60;MPOS=8;OCM=0;POPAF=2.40;SEQQ=23;STRANDQ=1;TLOD=2.05 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:3353,6:1.818e-03:3359:1667,3:1640,3:2113,1240,4,2 chrM 30 . T C . pon CONTQ=64;DP=17980;ECNT=29;MBQ=20,20;MFRL=165,159;MMQ=60,60;MPOS=30;OCM=0;POPAF=2.40;SEQQ=93;STRANDQ=5;TLOD=18.04 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:17311,65:2.009e-03:17376:8674,38:8437,26:10619,6692,42,23

so what's happened? I am appreciate for any help.

my mutect2 parameters are as below, I disable downsampling, I don't know if this introduce the matter?
/usr/local/gatk-4.1.4.0/gatk --java-options "-Xmx5g" Mutect2 -R /database/GATK_bundle/chrM/references_hg38_v0_chrM_Homo_sapiens_assembly38.chrM.fasta -I bwa/M627.rmdup_ref.bam -O mutect2/M627.m2_ref.vcf --bam-output mutect2/M627.m2_ref.bam --annotation StrandBiasBySample --mitochondria-mode --independent-mates **_--max-reads-per-alignment-start 0_** --max-mnp-distance 0

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