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Relevance of alignments filtering before variant calling

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?

filtering wgs alignment variant
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by qstefano • qstefano

1 answer

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.
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written by Pierre Lindenbaum Pierre Lindenbaum

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