Get all unmapped read and mate in bam
Hello,
I have a .bam file and i am trying to extract all combinations of unmapped read and its mate from it.
One type is unmapped read and its unmapped mate which i extract using,
samtools view -bh -f 12
where, read is unmapped and mate is unmapped
samtools view -bh -f 8 -F 4
where, read is mapped and mate is unmapped
samtools view -bh -f 4 -F 8
I would like to know if i'm doing it right? or am i missing something.
Thank you.
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Istvan Albert
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vinaykusuma •
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vinaykusuma •
1 answer
All looks good, and you can check that with samtools flags:
samtools flags 12
0xc 12 UNMAP,MUNMAP
samtools flags 8
0x8 8 MUNMAP
samtools flags 4
0x4 4 UNMAP
then as you show for flags:
-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]
the only comment I have is that when you produce BAM files the -h flag is not needed.
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