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 126.96.36.199-SNAPSHOT built at Tue, 30 Jun 2020 17:28:31 -0400.