Filter out unmapped reads
Category Read Filters
OverviewFilter out unmapped reads.
Unmapped reads are defined by three criteria:
- SAM flag value 0x4
- An asterisk for reference name or RNAME (column 3 of a SAM record)
- A zero value for leftmost mapping position for POS (column 4 of SAM record)
GATK version 18.104.22.168-1-gf548ccd-SNAPSHOT built at Mon, 2 Aug 2021 14:22:45 -0700.