Extract Reads From All Chromosomes Except One.

Question

[KCC]

I created a sam file by aligning reads, using bwa. I want to create a new sam file that contains all reads except ones that are on a particular chromosome or have an alternative alignment on that chromosome.

How can I do it?

Answer 1

[Rlong]

cat yoursam.sam | awk '{ if($3 != YourExcludedChrom) print $0 }'

That should do it.

EDIT: However, the alternate alignments to the excluded chromosome will still be in there. Sorry.

[KCC]

I ended up writing my own python script that filters lines in the SAM based on what chromosome they map to. So, your answer is best.