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I have a bam file of whole exome human data. I now want to check coverage of a list of genes in my data. Basically, I want to get output like, for example:

Gene    Percentage of coding region covered
A1BG               100 %
A1BG-AS1           100%
A1CF                99.94%
NEK8                100%
FANCI              100%
A2ML1             100%

I want to find out at which depth how much percentage of given genes are covered. for example AT 30X NEK8 gene covered 100%. Interested in the canonical transcript and if canonical transcript is not present then we can consider other transcript in that case.

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    $\begingroup$ Please edit your question and add more detail. How do you define "coverage"? Is one read enough? Do you want a minimum coverage? What transcripts of the gene? All of them? Only the canonical? What if there is no canonical? How do you define a gene? Are you also interested in UTRs? How about non-exonic regulatory regions which will probably not be included in WES data? $\endgroup$
    – terdon ♦
    Commented Apr 26, 2023 at 11:10
  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Commented Apr 26, 2023 at 11:41
  • $\begingroup$ I have edited the question and provide the information hope now its clear $\endgroup$
    – Ani
    Commented Apr 28, 2023 at 7:35
  • $\begingroup$ Thanks. So, what data do you have? How can we know the locations of these genes? How do we know what transcript to use? Do you have a bed file with the regions of interest? Also, again, how do we define coverage? Do you want the average coverage over the length of the gene? The maximum? The minimum? Do you want a report by exon? By the entire gene length? What is your minimum coverage threshold to consider something as "covered"? $\endgroup$
    – terdon ♦
    Commented Apr 28, 2023 at 10:37
  • $\begingroup$ I have a bam file of human whole exome data and also a bed file of all regions of interest. Yes i want the average coverage of gene at threshold 30x and report by gene. $\endgroup$
    – Ani
    Commented Apr 28, 2023 at 12:53

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