Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

ignoreFilter in VariantRecalibrator

BerntPoppBerntPopp Posts: 47Member
edited September 2013 in Ask the team

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...

Post edited by Geraldine_VdAuwera on

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