WES coverage

[przemekl]

Do you have any doubts about counting the coverage for the entire reference genes, even though, for WES, the coverage is present only in the coding regions?

[dlopez-bioinfo]

Hi przemekl, reference genes are used to normalize the average coverage for SMN1 and SMN2. As you pointed out, taking the whole gene length instead of the coding region would affect the average coverage calculation. However, SMAca don't use absolute values but the ratio with respect to SMN genes. The objective is to detect samples that deviate from the batch average, no matter what exactly that batch average really is. The only requirement is that the whole batch analysis must be sequenced with the same capture kit and technology (WES and WGS can't be mixed) and, if possible, at the same sequencing run.

[przemekl]

If we look at a specific case, gene SIL1 for example, average coverage ranges from 1.6 to 2.5 (25 WES samples) Are these values too low?
Besides, if we compare the coordinates (SIL1,hg38) chr.5:138.946.719-139.293.557 Shouldn't it be chr:5138946724-139.198.368 ncbi?
Of course, this fix won't significantly change average coverage.