extract interchoromosomal pairs from a BAM

[Tanharsh]

Hi,

Is there a faster tool to extract inter-chromosomal reads from a BAM file directly rather than using samtools view and awk '($3!=$7 && $7!="=")' statement?

Thanks.

[Tanharsh]

Anyone has some solutions regarding spilitting a huge bam like whole genome library? thanks.

[dpryan]

The only faster method would be to write something in pysam or using either the C htslib of java htsjdk APIs. Those are likely only faster due to not needing to format things for printing. Alternatively, you could write something that starts a different thread for each chromosome or, or divides things according to where there are known gaps, or...

There are a lot of ways to divide things, but realistically you're going to be limited by IO and decompression rate, since the actual processing you're doing is trivially fast.

[Tanharsh]

Hi,
Thanks for your reply. right now I am using different threas or fork as many intervals as I need. but interchromosomal pairs using the above awk statement takes a longer time for whole genome libraries. Any thoughts? Thanks.