Hi,
I have encountered an issue while running mitoHPC where some variants present in the mutect2.mutect2.00.vcf with allele frequency (AF) > 0.03 are being filtered out and do not appear in the mutect2.mutect2.03.vcf.
For example, the variant below is present in HG00428.final.mutect2.mutect2.00.vcf but is missing in mutect2.mutect2.03.vcf:
chrM 567 . A AC . PASS SM=HG00428.final;INDEL;Hypervariable=HV-III;Homopolymer;DLOOP GT:DP:AF 0/1:7030:0.148
Could you please provide guidance about why this might be the case, or if there is anything that can be done to fix this?
Thank you very much for your help.
Hi,
I have encountered an issue while running mitoHPC where some variants present in the mutect2.mutect2.00.vcf with allele frequency (AF) > 0.03 are being filtered out and do not appear in the mutect2.mutect2.03.vcf.
For example, the variant below is present in HG00428.final.mutect2.mutect2.00.vcf but is missing in mutect2.mutect2.03.vcf:
chrM 567 . A AC . PASS SM=HG00428.final;INDEL;Hypervariable=HV-III;Homopolymer;DLOOP GT:DP:AF 0/1:7030:0.148
Could you please provide guidance about why this might be the case, or if there is anything that can be done to fix this?
Thank you very much for your help.