Dear Biostars,

Is someone aware of a tool that can accept a bam and bed file with positions to investigate, where the tool returns a table which summarizes base calls by read?

This is with long reads in mind.

For example, the bed file could be;

chr1 10 10 site1 0 +

chr1 50 50 site2 0 +

And the output would be;

read1 site1 A

read1 site2 C

read2 site1 G

read2 site2 T

read3 site1 A

read3 site2 C

Thanks,

joe