Calculating Mapping Coverage

Question

[Hatem Elshazly]

Hi there,

Does anyone have any suggestions for a tool to calculate the mapping coverage (e.g. for each contig in the reference genome, how many reads are mapped against this contig)?

Also if any one can provide me with references covering this topic, I will be gratefully thankful.

thanks in advance.

Shazly

[Ashutosh Pandey]

See this link: Tools To Calculate Average Coverage For A Bam File?

Though this link is pretty old but you may still find some tools that may still exist. Search for coverage in the search window and you should be able to find lots of posts dealing with the same problem.

[Amitm]

Hi,

I would share my two cents of experience. Its straightforward to calculate mapping coverage using Bedtools but what I missed initially is that its not feasible to apply mapping quality, base quality, number of covering reads and similar filters using a simple approach like Bedtools. Its much better to use GATK DepthofCoverage and CallableLoci which can apply all those filters and give a "true" representation of coverage & depth. Look into their documentation plz.

Answer 1

[Brian Bushnell]

Using the BBMap package, you can do this with the Pileup tool:

pileup.sh in=mapped.bam out=stats.txt

That will give the number of reads mapped to each reference sequence, average coverage, percent of bases covered, standard deviation, etc.

Answer 2

[John Kern]

Hello Shazly,

bcbio is a "python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis".

We want to add coverage to the pipeline and are considering a new project called chanjo. I haven't done due diligence yet but you might want to check it out.

Regards,
John