Question: Using SomaticSniper to call variants in specific regions?
1
gravatar for sichan
3.7 years ago by
sichan70
Canada
sichan70 wrote:

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.

 

sequencing snp next-gen genome • 997 views
ADD COMMENTlink modified 3.7 years ago by Sean Davis25k • written 3.7 years ago by sichan70

Looks like it's not possible with SomaticSniper:

C: Find Mutations In A Region

ADD REPLYlink written 3.7 years ago by sichan70
0
gravatar for Sean Davis
3.7 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

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.

 

ADD COMMENTlink written 3.7 years ago by Sean Davis25k
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