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!
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.