Sequencing statistics

[tahamasoodi]

Hi,

May I know how can we calculate the following from whole genome/exome data?

Reads mapped to the human genome
Reads mapped to the target regions (exome)
Coverage of target regions at 1x
Coverage of target regions at 10x
Coverage of target regions at 50x

[aaronh]

GATK's DepthOfCoverage will do this.

[tahamasoodi]

Thanks, but it is giving results by position wise. I need the overall average. Is there anyway to do that in GATK.

[aaronh]

One of the files it generates: SAMPLE_NAME.sample_summary has that. The sample_cumulative_coverage_proportions file will tell you how much of the genome is covered by some X.

[tahamasoodi]

Ok, it is running now and i'm waiting for the results. Will it tell anything on the number of on target genotypes at a particular X?