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hisplan/samtools.md

Created January 29, 2019 16:54
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samtools
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samtools.md 
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 reversed
	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

  -f INT   only include reads with all  of the FLAGs in INT present [0]
  -F INT   only include reads with none of the FLAGS in INT present [0]
  -G INT   only EXCLUDE reads with all  of the FLAGs in INT present [0]

  -h       include header in SAM output
  -H       print SAM header only (no alignments
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