1,555
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Filtering According to Depth and Map Quality
--minMapQuality ''threshold'' Positions where the root-means squared mapping quality falls below this threshold will be excluded.
--minMapQuality ''threshold'' Positions where the root-means squared mapping quality falls below this threshold will be excluded.
--strict When the map quality is interpreted ''strictly'', all three trio individuals must exceed ''minMapQuality''
--strict When the map quality is interpreted ''strictly'', all three trio individuals must exceed ''minMapQuality''
before a call is made. Without the --strict option, reads for individuals below the threshold are ignored.
--minDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded.
--minDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded.
