how to evaluate coverage at a regions of interest and generate specificity, sensitivity and PPV for that region?

Question

[bioinforesearchquestions]

Hi guys,

We have exome sequenced samples at a minimum of 15X coverage using capture kits.

• We would like to
  • identify genes that may have low coverage because no probes are available
  • identify gene that falls within a region which is difficult to sequence by the capture kit
• how to evaluate coverage at a regions of interest and generate specificity, sensitivity and PPV for that region?
• how to develop statistics based on the existing samples of how well the samples provide on-target coverage, uniformity and ability to detect single nucleotide variants (SNVs), insertions and deletions (indels) and copy number variants (CNVs) in the region of interest.
• Is there any statistics which is already developed?

Kindly experts throw some light on the above queries.

[h.mon]

Do you have a bed file with exome probes? If you do, you can use bedtools to achieve several of your goals:

identify genes that may have low coverage because no probes are available

Use bedtools intersect -v with the genome annotation to get the genes / exons not covered by the probes.

how to evaluate coverage at a regions of interest

Use bedtools coverage.