Samtools question

[lre1234]

Hi all,

I'm relatively new to analyzing sequence data, and have a question about using samtools for SNP calling from exome data. When going from a bcf file to a vcf file, is there a way to set a limit that it will only make the SNP calls at base positions that have a minimum read depth. For example, if I only want SNPs to be called when a base has a read depth of 10x or greater, is there a specific flag for this, or would this be done by filtering through the vcf file afterwards? The samtools documentation is not completely clear to me.

Thanks for your help...

[Heisman]

I don't see an easy way to do it. Probably easier to just filter after the fact (that's what I do).

[liying]

Enter:
vcfutils.pl varFilter
The detail will be shown on screen.
-d 10 is what you want.