VariantFiltration more SNPs in output file than in input file
Dear GATK team,
Thank you for the GATK software package and the great documentation which is very helpful!
However, I observed that after filtering my VCF file includes more variants than before. As I understood, the same number of Variants should remain, only on some of them will be tagged with e.g. "LOWQUAL".
How should I interpret that? I checked one of the variants which was there in the filtered but not in the unfiltered. It is a LOWQUAL-tagged SNP.
Thanks a lot for your help!