estimate error profile from aligned Illumina reads

Question

[Richard]

Hi folks, Can anyone recommend a tool that can loop through a BAM file and give me information about which base substitutions are present at each position in the reads?

Ideally, it would report a table that would give the estimate error rate at each read position.

Answer 1

[michael.ante]

Hi Richard,

RSeQC's mismatch-profile can do this. The result table is stored in a tab-separated file which has the misleading extension xls.

Cheers

Michael