Hi, I'm using the recently released Mutect2 and one of the failure reasons I found in my vcf is "homologous_mapping_event". What is this filter based on? is there any parameter linked to it?
Thanks for your help.
The VCF header should contain description lines for each of the filters. For this filter you should see the line "More than three events were observed in the tumor". Based on the code I believe this specifically refers to three events located in cis on a haplotype. Such a configuration suggests the reads supporting the alt alleles may simply be mapped to the wrong one of multiple homologous regions. There is no parameter available to modify the behavior of this filter; the threshold number is hard-coded.