Exclude variants in certain regions

[OlgaMikh]

Hi all,
I would be very greatful if somebody can advise me software which could exclude SNPs at known regions. My problem are the SNPs in primer sequences, I have to exclude them out my further analysis.

Thanks a lot.

[swbarnes2]

If you have a .bed file of your primer locations, BEDTools can intersect a .vcf with a bed file, so you'll only get the .vcf entries not in the regions of the .bed.

You could align your primers to the genome with bwa or bowtie or whatever, and convert the .bam to .bed with BEDTools.

[Heisman]

You might want to look into the varscan limit utility