Hi all. I need to find the coordinates for every point mutation for EACH READ in a bam file. The coordinates should be expressed as both (1) the position of the mutation in relation to the read length and (2) the position of the mutation in relation to the chromosome coordinates.
Also, for each point mutation I need to output the reference base pair and the mutated base pair.
Samtools mpileup outputs interesting info, but I would need them for EACH READ rather than piling up reads at a single genomic position.
Would you suggest to write my own script or are there already functions I can use?