Number of SNPs by target sequencing

Question

[MAPK]

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?

Answer 1

[Nicola Casiraghi]

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 ftp://ftp.ncbi.nih.gov/snp/organisms/

Finally you can exploit bedtools to "determine number of SNPs captured by each of these targeted method" :

bedtools intersect -a dbSNP  -b mypanel.bed

[Keith Callenberg]

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:

1. Download the Illumina TruSight bed as Nicola mentions above.
2. Download the COSMIC coding mutations VCF from http://cancer.sanger.ac.uk/cosmic/download (requires registration)
3. (optional) A few of the TruSight panels cover non-coding regions as well. If this is the case for your panel, you may want to also download the non-coding COSMIC VCF, and merge the two together.
4. Run bedtools intersect with the COSMIC VCF in place of dbSNP above.

[Nicola Casiraghi]

Correct, or refer to the ClinVar dataset from NCBI.