I am running CombineVariants followed by VariantEval on two VCF files (GATK version 3.1-1). I noticed that none of my "set=FilteredInAll" variants are included in the output of VariantEval. I suspect this is because the FILTER column is not "PASS" because the variants were not "PASS" in either of the input VCF files.
Is there an argument to pass into VariantEval so that it does not filter variants out based on the FILTER column? I was using the arguments from a guide article (http://gatkforums.broadinstitute.org/discussion/48/using-varianteval). I saw that in the comments you mentioned an --ignoreFilters argument, but when I tried to use it I got the GATK error: Argument with name 'ignoreFilters' isn't defined.
I can just change the FILTER column entries in the combined VCF file, but it seems like a problem that others might have as well.
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...