This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
ignoreFilter in VariantRecalibrator
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...