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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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call on poolseq #1174

Open crougeux opened 4 years ago

crougeux commented 4 years ago

Hi, I am calling SNPs in several dataset. I am giving a try to BCFtools mpileup and call to wgs-data. I was wondering if I could use the same approach with pool-seq data? I could control for the ploidy level to integrate the number of individuals... Is BCFtools call able to deal with pool-seq data and what are the specificities??

Thanks in advance!!!

pd3 commented 4 years ago

I am not familiar with pool-seq data. I am assuming it's just extreme low coverage but otherwise the samples are correctly annotated in the bams? Or is it more like a metagenomics problem where individual reads are not tagged by an individual? If the first, an approach like this might work https://github.com/samtools/bcftools/issues/1168. If the latter, bcftools does not support ploidy bigger than 2 and you'll have to look elsewhere.