Question: how to evaluate coverage at a regions of interest and generate specificity, sensitivity and PPV for that region?
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3 months ago by
United States
bioinforesearchquestions180 wrote:

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.

ADD COMMENTlink modified 10 weeks ago by Biostar ♦♦ 20 • written 3 months ago by bioinforesearchquestions180
1

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.

ADD REPLYlink written 3 months ago by h.mon20k
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