Relevance of alignments filtering before variant calling

Question

[qstefano]

Hello everyone,

Searching the literature, I noticed that in several (many) papers or bioinformatic pipelines, no filtering of alignments is performed, but why? I personally discard alignments with at least MAPQ<20 before performing variant calling, What do you think?

Answer 1

[Pierre Lindenbaum]

I noticed that in several (many) papers or bioinformatic pipelines, no filtering of alignments is performed

IMHO, this is wrong, people calling with gatk HaplotypeCaller have a default filter on MAPQ=20

--minimum-mapping-quality:Integer
                              Minimum mapping quality to keep (inclusive)  Default value: 20.