Moving up ability to set mismatch quality related filter thresholds to the input YAML #169
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Moving up the
max_mm_qualsum_diff
andmax_var_mm_qualsum
arguments used by the fpfilter through the following WDLs.somatic_exome_nonhuman.wdl
detect_variants_nonhuman.wdl
subworkflows/mutect.wdl
subworkflows/strelka_and_post_processing.wdl
subworkflows/varscan_pre_and_post_processing.wdl
subworkflows/fp_filter.wdl
tools/fp_filter.wdl
Noticed that we needed this functionality for a situation where we didn't have a matched normal (as is often the case for non-human experiments), and were not calling a real KRAS G12 variant due to (germline) mismatches in the positions around the variant resulting in us failing variants with flags
MMQSD50
andMMQS100
set by themax_mm_qualsum_diff
andmax_var_mm_qualsum
thresholds.