Question: Counting Read Support At A Particular Position Of A Bam File
3
gravatar for Shaun Jackman
5.9 years ago by
Shaun Jackman420
Vancouver, Canada
Shaun Jackman420 wrote:

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

vcf bam samtools genotype • 4.5k views
ADD COMMENTlink modified 5.9 years ago by Chris Miller20k • written 5.9 years ago by Shaun Jackman420

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

ADD REPLYlink modified 5.9 years ago • written 5.9 years ago by Pierre Lindenbaum119k
2
gravatar for Chris Miller
5.9 years ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

Sounds like you want bam-readcount: https://github.com/genome/bam-readcount

ADD COMMENTlink written 5.9 years ago by Chris Miller20k

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 REPLYlink written 5.9 years ago by brentp23k

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 REPLYlink written 5.9 years ago by Shaun Jackman420
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