Question: Number of SNPs captured by targeted sequencing panels
gravatar for MAPK
4.7 years ago by
MAPK1.7k wrote:

I am trying to find the approximate number of SNPs from each of these capture methods:

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

targeted sequencing • 897 views
ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by MAPK1.7k
gravatar for rbagnall
4.7 years ago by
rbagnall1.7k wrote:

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
ADD COMMENTlink written 4.7 years ago by rbagnall1.7k

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.

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by MAPK1.7k

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.

ADD REPLYlink written 4.7 years ago by rbagnall1.7k
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