Question

Counting Read Support At A Particular Position Of A Bam File

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11.5 years ago

Shaun Jackman ▴ 420

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 • 7.8k views

ADD COMMENT • link updated 11.5 years ago by Chris Miller 22k • written 11.5 years ago by Shaun Jackman ▴ 420

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

ADD REPLY • link 11.5 years ago by Pierre Lindenbaum 164k

Ram · Answer 1 · 2013-05-13

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11.5 years ago

Chris Miller 22k

Sounds like you want bam-readcount.

ADD COMMENT • link updated 5.1 years ago by Ram 44k • written 11.5 years ago by Chris Miller 22k

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

ADD REPLY • link 11.5 years ago by brentp 24k

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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

ADD REPLY • link 11.5 years ago by Shaun Jackman ▴ 420