Filter Alignments for unmapped pairs
- An unmapped read whose mate is mapped.
samtools view -u -f 4 -F264 alignments.bam > tmps1.bam
- A mapped read who’s mate is unmapped.
samtools view -u -f 8 -F 260 alignments.bam > tmps2.bam
- Both reads of the pair are unmapped.
samtools view -u -f 12 -F 256 alignments.bam > tmps3.bam
