Compare difference capture technologies

[bobjackal]

Please let me know if I'm posting in the wrong place.

My question that since there are so many different exome capture technologies, is there any tool for comparing all of them ?

My purpose is that we have a list of variants (SNP) across whole genome, and we want to know which exon capture technology can cover most of them. Is there any tool can do this ?

I know that I can of course try to customize the capture region just like target-re-sequencing, but it's not very cost efficient.

Can anyone help ? Thank you so much.

[ECO]

Easiest way is to get coordinates of your snps and use bedtools to intersect with each exome provider's target set (which are readily available from their website).

Pick the one that covers the broadest part of your target set, and design and spike in DNA probes to cover those targets that the exome kit misses.

[bobjackal]

Thank you ECO,

I have tried the intersect function of bedtool. It seems can provide some basic information of my problem. However, is this the only one way to do that ?
Because the further question is that I want have a comparison which is from region to region.

Let's say, if I have the exon information on a list of gene, how can i know the proportion of being covered by one particular capture method ? What I'm doing is that

1. have a script to get the (.bed) exon information of each gene
2. compare to the capture region by bedtool intersect function
3. calculate by excel because the intersect function can only show the overlapping region.

Am I on the right track ? Is there any other possibility ?