Sequence Capture Compared To Next Genome Sequence As Quality Control

Question

[Houkto]

Hi all,

we are thinking of comparing Next-genome-sequence (from two animal strains with coverage ranging from X21-26) with sequence capture of targeted regions of the same strains (but with high coverage X10,000) as a quality control. Both data were analysed using the same pipeline.

The current approach we are thinking of using is: extract the SNPs from NGS data SNPs/indel using the targeted regions that were used in the custom sequence capture and then compared how many snps were missed by NGS analysis.

It would be nice to know what do you think of this approach and is there another way to achieve quality control ?

Thanks

Answer 1

[Zev.Kronenberg]

Sanger verifying some SNVs would give you false positive rates.

[Houkto]

Indeed, however, we are trying to make a use of the high coverage of sequence capture. Any thoughts ? and what is your impression of using seq capture as quality control?