How do I change the settings in qualimap (bamqc) to consider only the exome length in every chromosome instead of entire chromosome length

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8.4 years ago

bioinforesearchquestions ▴ 370

Dear all,

We have exome sequenced samples. I am planning to get the statistics for these exome samples using qualimap bamqc.

Actually, the mean coverage (2.28X) seems to be very low and also the coverage for every chromosomes i.e. around 1.5-3X. Then only I realized that the tool should consider only the length of exome in every chromosome instead of the entire chromosome length.

Considering the below exon length for calculating coverage (729,599,759 bases/8,079,409 exon bases = 90X coverage). **Is my understanding correct?

How do I change the settings in qualimap (bamqc) to consider only the exome length in every chromosome instead of entire chromosome length?**

Chr Total-Bases Exon Bases

chr1 249250621 8079409

chr2 243199373 5781424

chr3 198022430 4706998

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sequencing bamqc bam coverage • 2.5k views

ADD COMMENT • link 8.4 years ago by bioinforesearchquestions ▴ 370

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Did you ever find a solution? I have the same issue.

ADD REPLY • link 7.9 years ago by dana107 • 0

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No, Have you got a chance to work on this?

ADD REPLY • link 7.2 years ago by bioinforesearchquestions ▴ 370

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