Precision of variant calling (INDELs)

Question

[esimonova.me]

The same sample (NA12878) was sequenced as WES and WGS, and analysed by the same pipeline (in case of WES it was restricted to the bed size). The precision for WES was lower by 2 % than for WGS and I have no explanation for that. Could library preparation influence that?

Thanks

[desouzareis.r]

Hi, yes it could. You can compare coverage between them, especially in regions where there are false positive and false negative variants resulted from the comparison. VCFEval for example generates the files fp.vcf and fn.vcf that you can look at.