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Hi, I don't see none of the chromosome have 1/1 homozygous alternate in both NORMAL and PRIMARY.
Downloaded sample from TCGA data from broad institute.
FILTER=<ID=mf1,Description="Filtered out by MuTect v.1">
FILTER=<ID=oxoG3,Description="Filtered out by OxoG Artifact Filter v3">
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL PRIMARY
1 14464 . A T 47 mf1 DP=85;MQ0=0;SS=Germline;VT=SNP;VLSC=. GT:AD:DP:FA:MQ0:BQ:SS:SSC 0/1:37,23:60:0.383:0:32:1:. ** **0/1:9,16:25:0.640:0:29:1:.
1 14542 . A G 12 mf1 DP=138;MQ0=0;SOMATIC;SS=Somatic;VT=SNP;VLSC=. GT:AD:DP:FA:MQ0:BQ:SS:SSC ** 0/0:103,5:108:0.046:0:33:2:. 0/1:24,6:30:0.200:0:26:2:.**
Please help me to understand it. Is it because of OxoG Artifact Filter?