Calculating coverage for WGS, WES and RNASeq

Question

[Joshi]

Hi,

I need some advise on calculating coverage

Basically for a set of BAM files, WGS, WES and RNA-Seq - I am interested in calculating and representing coverage - to show the contrast between these differing sequencing techniques (and limited to that ... not comparison). The coverage needs to be calculated at gene/exon level.

I am comfortable enough with determining the region of interest and extracting those regions from NCBI's Refseq.

However, I would appreciate some guidance around various coverage metrics for WGS, WES and RNA-Seq and what characteristics and limitations they have.

Needless to say, I am willing to do the background reading - but some guidance in this matter will help me understand the landscape.

Thanks, Himanshu

Answer 1

[finswimmer]

Hello,

my favorite is picard HSMetrics. There is also a detailed description of the metrics.

fin swimmer

Answer 2

[trausch]

You can try alfred (disclaimer: our own tool). Example plots are here: WGS and WES. It also supports feature counting for RNA-Seq.

Answer 3

[Philipp Bayer]

There's also mosdepth

The manual shows different options for exome/WGS etc. input, you can use a bed file of regions of interest to see only those. Preprint from 6 days ago: http://www.biorxiv.org/content/early/2017/09/07/185843