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Old 10-29-2013, 08:05 AM   #1
Coru S
Junior Member
Location: Germany

Join Date: Oct 2013
Posts: 4
Default How to extract base coverage from bam/bai-files

Hi Everybody,

I'm still quite new to the world of next-generation sequencing. I started to work with the Ion Torrent PGM several months ago.
I've got a question related to the analysis of the coverage depth of different nucleotides/dels/insertions on the base positions of my reads.

I normally use the bam and corresponding bai-files generated by the Torrent Suite Software and load them into the IGV-Genome Browser.
There, one can get information about single base position coverage by mouseover (see screenshot).

One can see the total base count, count of A/T/G/Cs (+ and - reads), and count of dels and insertions.
I would like to have this data in a table, to use it in an Excel spreadsheet.

Can anybody tell me, how I can extract this data from my bam/bai-files for a defined region of interest? I'd appreciate any hints.
The most preferred output would be a data table like this:
chrom position total count count of:A+ A- T+ T- C+ C- G+ G- del+ del- ins+ ins-
chr13 33211005 50 20 21 2 3 0 0 0 0 2 0 1 1

I've searched the forums for related threads, but I only found some bioinformatic information that I couldn't understand. I'm just a biochemist, and I have no big skills in bioinformatics. E.g., I don't know about Linux OS and how to use software or commands there.
Any help is much appreciated.

Thank you very much in advance.
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