I am trying to find the number of SNPs captured by each of these sequencing panel listed here: http://www.illumina.com/products/trusight-panels.html . Can someone please tell me how I can determine the number of SNPs captured by each of these targeted method?
First, you should retrieve the BED file with targeted regions for each panel: for example for panel TruSight One Sequencing Panel Kits you can find the link to BED file Access the gene list and other product files » in section Product Configurations. The BED file for this panel is named TruSight One File for UCSC Browser (BED Format)
Once you retrieved your panel in BED format, download the preferred version of the dbSNP catalogue (VCF or BED format) for the Human genome at
Finally you can exploit bedtools to "determine number of SNPs captured by each of these targeted method" :
bedtools intersect -a dbSNP -b mypanel.bed