How can I filter out reads who or whose pairs are unmapped in samtools?

[maimaiti2008]

How can I filter out reads who or whose pairs are unmapped in samtools?

I tried using "samtools view -F 4 -F 8 SAMFILE". However, this command just allows filtering out those whose pairs are unmapped (only "-F 8" is effective).

I wonder if it is possible to do the job in one command.

[jimmybee]

How can I filter out reads who or whose pairs are unmapped in samtools?

I tried using "samtools view -F 4 -F 8 SAMFILE". However, this command just allows filtering out those whose pairs are unmapped (only "-F 8" is effective).

I wonder if it is possible to do the job in one command.

um do them one at a time

samtools view -bS -F 4 -o OUTBAM_mapped SAMFILE
samtools view -bS -F 8 -o OUTBAM_unmapped SAMFILE

you can do "samtools merge" to combine them for analysis if thats what you're after