Number of SNPs captured by targeted sequencing panels

Question

[MAPK]

I am trying to find the approximate number of SNPs from each of these capture methods: http://www.illumina.com/products/trusight-panels.html

Can someone please tell me the number of SNPs we can capture from each of the methods mentioned in the link above?

Answer 1

[rbagnall]

We have used the Tru Sight Cardio sequencing ket. Variant calling is performed on the target regions +50 bp either side using GATK with hard filters. Here is an example of the variant numbers. Males may appear to have slightly more homozygous calls because there are X linked genes (hemizygous in males).

Sex     Het  Hom  Ancestry
Male    322  280  European
Female  369  234  European
Female  346  244  European
Male    359  264  European
Male    365  276  SouthAsian

[MAPK]

Thanks. Do you know if we can garner more than 10,000 SNPs from any of the methods in the link above? I think TruSight One would be the best bet for this as it captures 4800 genes.

[rbagnall]

That would be your best bet, but I don't know if you would reach 10,000 SNPs. Perhaps try intersecting the 4800 TruSight One genes with an exome dataset to see how many SNPs you may expect.