Keep only reads with a valid alignment start
Category Read Filters
OverviewKeep only reads with a valid alignment start (POS larger than 0) or is unmapped.
See MappedReadFilter for criteria defining an unmapped read.
See these additional references.
GATK version 184.108.40.206-1-gf548ccd-SNAPSHOT built at Mon, 2 Aug 2021 14:22:45 -0700.