Question: Reference And Alternative Allele Count
2
gravatar for gabrielle123123
8.3 years ago by
gabrielle12312320 wrote:

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

allele reference • 5.0k views
ADD COMMENTlink modified 8.0 years ago by Erik Garrison2.3k • written 8.3 years ago by gabrielle12312320
1

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/

ADD REPLYlink written 8.3 years ago by Zev.Kronenberg11k
3
gravatar for matted
8.3 years ago by
matted7.3k
Boston, United States
matted7.3k wrote:

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.

ADD COMMENTlink written 8.3 years ago by matted7.3k
0
gravatar for Malachi Griffith
8.3 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith18k wrote:

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

ADD COMMENTlink written 8.3 years ago by Malachi Griffith18k
0
gravatar for gabrielle123123
8.3 years ago by
gabrielle12312320 wrote:

Thanks, i will look at those option

ADD COMMENTlink written 8.3 years ago by gabrielle12312320
1

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ADD REPLYlink written 8.3 years ago by Malachi Griffith18k
0
gravatar for Erik Garrison
8.0 years ago by
Erik Garrison2.3k
Napoli, IT / UCSC
Erik Garrison2.3k wrote:

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.

ADD COMMENTlink written 8.0 years ago by Erik Garrison2.3k

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

ADD REPLYlink modified 8.0 years ago • written 8.0 years ago by Zev.Kronenberg11k

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

ADD REPLYlink written 8.0 years ago by Erik Garrison2.3k
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