Using SomaticSniper to call variants in specific regions?

Question

[sichan]

Hello,

I'm using SomaticSniper version 1.0.4 to call somatic variants in my tumor/normal paired BAMs. I don't think it's possible to call SomaticSniper in a specific region in my BAMs, correct? There doesn't seem to be an option for the user to specify a BED file for SomaticSniper to call variants in.

One way to get around this would be to pull out the reads aligning to regions of interest in the paired BAMs, but I'd rather not do that.

Thanks

[sichan]

Looks like it's not possible with SomaticSniper:

C: Find Mutations In A Region

Answer 1

[Sean Davis]

You could consider using samtools view with a region file and then including that inside a bash IO redirection like so:

somaticsniper .... <( samtools view -R bedfile.bed tumor.bam ) <( samtools view -R bedfile.bed normal.bam )

I have not tried this, but it might do the trick.