about mapping quality in GenomeSTRiP

Bazinga199122Bazinga199122 BeijingMember

I am using GenomeSTRiP to call deletions, I want to know how to set the threshold of mapping quality of my reads(for example 20). Can anyone help me with that? Thanks a lot!

Answers

  • bhandsakerbhandsaker Member, Broadie, Moderator admin

    To change the mapping quality threshold used in deletion discovery, use "-P select.minimumPairMappingQuality:20".

    There is a different setting to control the mapping quality filter used in genotyping: "-P pairs.minimumMappingQuality:20".

    See also conf/genstrip_parameters.txt.

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