Question : Plotting Per Chromosome/All Chromosome Coverage From Ngs Bam File

Question

[thecuriousbiologist]

Hi,

I wish to plot per chromosome coverage from a BAM file obtained from aligning exome sequencing data.

Are there any good R packages/any other non-R packages that can quickly get me such plots ?

I was planning to use samtools to generate pileup files and then go on from there, however that would take a long time.

Any suggestions would be much appreciated.

Thank you.

Answer 1

[William]

Qualimap is a very good and easy to use quality assurance tool for use on BAM files. It gives you a lot of statistics and plots, including coverage on all the chromosomes, in numbers and in plots.

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

[thecuriousbiologist]

Thanks. Yes, I did finally move on to Qualimap. I ran it on some small datasets and the reports look good. !

Answer 2

[thecuriousbiologist]

When Qualimap reports the per chromosome mean coverage, does it normalize by the size of the chromosome ? I have certain chromosomes where I always get a low coverage as compared to others ?

[William]

It is the mapped bases divided by the length of the chromosome ( the previous 2 columns). Maybe it is a more difficult chromosome to sequence / map.

http://qualimap.bioinfo.cipf.es/doc_html/analysis.html#bam-qc

[Fennan]

Please note that if an annotation is provided, since version 0.7 the coverage will be normalized by the length of all the regions in the corresponding chromosome. Please see this thread for more information: https://groups.google.com/d/msg/qualimap/AO_6111Gg1E/-oey1kAs6GcJ

Answer 3

[Gabriel R.]

You can just put the depth column from mpileup into a text file and use the density() function in R to plot it. If you have to do it over and over again, write yourself a little perl script.