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?
Since a lot of the TruSight panels are designed for cancer, you might not be interested in all SNPs, but only cancer-related SNPs. If this is the case, you might want to use COSMIC instead:
bedtools intersect
with the COSMIC VCF in place of dbSNP above.Correct, or refer to the ClinVar dataset from NCBI.