Hello dear GATK Team,
it seams that the ignoreFilter Argument in VariantRecalibrator does not work. I want to include variants with LowQual filter in the calculation, but cant find the right way to do it. I tried all of these:
-ignoreFilter LowQual -ignoreFilter [LowQual] -ignoreFilter "LowQual" -ignoreFilter "Low Quality" -ignoreFilter Low Quality -ignoreFilter [Low Quality]
and also with --ignore_filter instead of -ignoreFilter.
Found 2 solutions:
1) Remove the LowQual filter with VariantFiltration and "--invalidatePreviousFilters"
2) "-ignoreFilter LowQual" has to be applied to ApplyRecalibration also...