Extract Reads From A Bam File That Fall OUTSIDE A Given Region

Question

[irfanwustl]

Using samtools view -L FILE command we can extract reads which are in the FILE regions. Is there a way to extract reads which are OUTSIDE of the FILE regions?

Thanks

[iraun]

I would suggest 2 options: 1) Create a bed file with the complementary regions to your current region file and run samtools with that new bed file. 2) Use bedtools intersect, applying -v argument.

Answer 1

[Pierre Lindenbaum]

samtools view -L in.bed --unoutput out.bam in.bam > /dev/null