Bbasereader

Retrieve all bases aligned to particular positions of sorted bam files. bbasereader provides read id, base and position.

Installing Bbasereader:

Compile the binary from the source and copy the binary to your favourite location.
See here about how to compile Rust source code.

Running Bbasereader:

bbasereader -p Position-of-interest -f Bam.file.bam > output.tsv
Where -p is the position you want to retrieve (with regards to the reference) and -f is the indexed bam file you want to explore.

Output

You will get a tsv with 2 columns, the read-id and the base it contains on the position of interest.