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Counting Read Support At A Particular Position Of A Bam File

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

bam vcf genotype samtools
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updated by Chris Miller Chris Miller • written by Shaun Jackman Shaun Jackman

1 answer

Sounds like you want bam-readcount.

• 42 views • link
updated by Ram Ram • written by Chris Miller Chris Miller

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

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written by brentp brentp

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