Counting Read Support At A Particular Position Of A Bam File

Question

[Shaun Jackman]

I have deep sequencing of an amplicon (~1,000,000x), and would like to count the number of reads that show an A,C,G or T at a particular position of a BAM file. I'm not concerned with indels currently. I have previously used the fifth column of samtools mpileup, but due to the high depth, this format is not ideal. Which other tools can you suggest? Is there a standard way to store this read-support information in a VCF file?

Thanks,
Shaun

[Pierre Lindenbaum]

related position of mismatches per read from a sam/bam file ?

Answer 1

[Chris Miller]

Sounds like you want bam-readcount.

[brentp]

that tool seems like it could be useful, but needs some docs describing what it is, what it does, and how to use it.

[Shaun Jackman]

bam-readcount works like a charm! Thanks, Chris. A warning though: by default it limits the maximum read depth to 8,000 reads, similar to samtools. I've opened a ticket on GitHub: https://github.com/genome/bam-readcount/issues/3