Wgs Coverage

Question

[hellbio]

Hi,

I would like to find out the coverage of a whole genome sample, (i need a value like 30X). For this i have used GATK to calculate the depth of coverage with the following command:

GenomeAnalysisTK.jar -R ref.fasta -T DepthOfCoverage -I input.bam -o out.txt

The output looks like

Locus Total_depth Average_depth Depth _for_sample

chr1:252053 93 93.00 93

chr1:252054 94 94.00 94

chr1:252055 91 91.00 91

chr1:252056 91 91.00 91

chr1:252057 91 91.00 91

chr1:252058 91 91.00 91

.

.

.

chrX:123834044 9 9.00 9

chrX:123834045 8 8.00 8

I have calculated the mean for the Total_depth (second column) across all the chromosomes and it gives 101. Does this mean that the sample depth is 101X? Could someone comment if im interpreting wrong.

[Ashutosh Pandey]

Yup for informal purpose you can say that you have an average coverage of 100x.

Answer 1

[William]

You can use qualimap to get more detailed information about your coverage:

http://qualimap.bioinfo.cipf.es/

[hellbio]

thanks for the info. Here i would like to know whether my interpretation is correct or not

[William]

I don't know. But I do know that you shouldn't need to do any calculations yourself to find out the whole genome coverage for a sample.