Reference And Alternative Allele Count

Question

[gabrielle123123]

Hi, I'm working on polypoid plant. Where using samtools and BCF tools to call SNP. We realize that bcftools have difficulty calling some simplex genotype and i would like doing it on my own. Is there a way to extract the number of reference and alternative allele from a mpileup format?

Thanks,

Gabrielle

[Zev.Kronenberg]

It might be worth checking out other variant calling software. For example I have been using SNVer for pooled and non diploid data. http://snver.sourceforge.net/

Answer 1

[matted]

See this post to get most of the way there using samtools mpileup. The other suggestion to consider other SNP callers is good too. I recall that FreeBayes can handle arbitrary ploidy, but I don't have any personal experience with it.

Answer 2

[Malachi Griffith]

You can use Bio::DB::Sam to get reference and alternative allele counts directly from a BAM file.

Answer 3

[gabrielle123123]

Thanks, i will look at those option

[Malachi Griffith]

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Answer 4

[Erik Garrison]

Rather than hacking samtools to handle polyploid detection, I would suggest using FreeBayes. It's designed to detect SNPs, indels, and complex variants (such as MNPs and other block substitutions) without restriction of ploidy.

I'm the author, so please email me if you have any questions.

[Zev.Kronenberg]

Can you call multiple bam simultaneously? IE strait to a multi individual vcf? Are you in the Marth lab?

[Erik Garrison]

Yes, I'm in the Marth lab. FreeBayes goes directly from (potentially 10s of thousands of) BAMs to a multi-sample VCF.