Exome not fully covered in WGS

[tahamasoodi]

Hi,

We are sequencing both exome and whole genome at 30x coverage. I used exome coordinate bed file to intersect it with the Whole genome bam file in order to extract the exome from the whole genome. To my surprise, I got only 8 million reads of exome from the WG whereas our exome sequencing produces around 40-45 million reads. However the coding variants from this are almost same as the exome (20-22 thousands). May I know why is it like this?

[jimmybee]

So just to be clear, you are running target exome capture and sequencing that on an Illumina machine, and sequencing whole genome shotgun on a similar machine?

The shotgun genome data contains things other than genes ie. repeats, non-coding DNA, intergenic sequence etc, whereas in a targeted exome sequencing procedure you only have the exome. You capture the same coding variants in both experiments, but the whole genome shotgun exome will be at a far lower coverage

[tahamasoodi]

But we are sequencing the whole genome at 30x, so it should cover the exome also at 30x.

[jimmybee]

Are you doing producing the same amount of data for exome and WGS?

[swbarnes2]

But we are sequencing the whole genome at 30x, so it should cover the exome also at 30x.

By my rough calculations, 8 Mreads that are 150 long would cover a 50 Mb exome at about 30x

50 Mreads of 100 bp each cover a 50 Mb exome at 100x.

How did you determine that you really have 30x coverage for each sample?

[tahamasoodi]

I calculate this by multiplying total reads by read length divided by 3000000000 (human genome size).