samtools

samtools flags

samtools flags

Version:
1.3
Identifier: TL_ec2a8d_4e.0b
Tool

Description


samtools flags INT|STR[,...] Convert between textual and numeric flag representation. FLAGS: 0x1 PAIRED paired-end (or multiple-segment) sequencing technology 0x2 PROPER_PAIR each segment properly aligned according to the aligner 0x4 UNMAP segment unmapped 0x8 MUNMAP next segment in the template unmapped 0x10 REVERSE SEQ is reverse complemented 0x20 MREVERSE SEQ of the next segment in the template is reverse complemented 0x40 READ1 the first segment in the template 0x80 READ2 the last segment in the template 0x100 SECONDARY secondary alignment 0x200 QCFAIL not passing quality controls 0x400 DUP PCR or optical duplicate 0x800 SUPPLEMENTARY supplementary alignment

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