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Can I bypass the MappingQualityUnavailableFilter in Unified Genotyper?
I'm trying to get counts of alleles from alignments generated by the Bismark bisulfite mapper, but Bismark sets MAPQ to 255 for all alignments. I'm not trying to do genotyping but would like vcf output to look at allele counts at different sites. Is there an option to gatk to skip the MappingQualityUnavailableFilter?