Samtools flagstat unpaired reads

Question

[rbronste]

Trying to quickly remove reads samtools flagstat deems as unpaired from BAM file? Thanks.

[GenoMax]

Have you searched Biostars (use external google search) for past threads? There has to be something available already.

Answer 1

[Pierre Lindenbaum]

remove unpaired files = reads that are not part of a paired-end experiment ?

samtools view -f 1 -b -o out.bam in.bam

[rbronste]

Yes just for BAM files already processed for removal of duplicates (Picard) and ChrM and ChrUN reads.