Samtools view filter by reference sequence

Question

[maxrwjones]

Hi all,

Just wondering if I'm missing something very obvious. I have a SAM file of a bunch of alignments mapped to a reference genome consisting of multiple chromosomes.

I can see from the samtools view man page how to include alignments by ref seq name in the output, but is there a way to exclude alignments by ref seq name? (I know I could do this with a pipe to grep or awk but I figure there must be a way to do it within samtools...) (I could also do it by just listing all the chromosomes I want except the unwanted ones, but that seems clunky and less portable to new scenarios.)

Cheers in advance!

Answer 1

[Pierre Lindenbaum]

get the complement BED use bedtools complement and the scan the bam using

samtools view  -L complement.bed 

[maxrwjones]

Thanks for your answer, I will give this a go!