Questions regarding extracting ref or non-ref allele counts in bam files.

Question

[mangfu100]

Hi all

I want to extract reference allele count or non-reference allele count with strand information using mpileup.

Before using mpileup, I treid to understand its options and functions but there are some options I didn't get it.

First, what is -C options?

Although I have read its explanation and examples, I don't know how to use it and why it is necessary to extract allele count.

Otherwise, Could you give me a recommended command to extract ref allele count using mpileup?

There are too many arguments in mpileup and I don't know which one to choose.