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alachins / raisd

RAiSD: software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors
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Input vcf file #13

Closed palomo11 closed 4 years ago

palomo11 commented 4 years ago

Hi,

I would like to detect selective sweeps in a set of bacterial genomes, and RAiSD seems as a perfect tool for it. But I have a question about the input vcf file I should use to run RAiSD.

The bacterial genomes (or more precisely metagenome-assembled genomes) were recovered from 12 drinking water treatment plants (2 samples per plant). Therefore, I have 24 bam files. To get the vcf I was thinking to use freebayes (any other recommendation?). The question is if I have to get 1 vcf per bam file, or I should run freebayes in multi bam mode to get only 1 vcf (for each genome).

alachins commented 4 years ago

Hi there, You need to create only 1 vcf file containing all the samples you want to include in the analysis with RAiSD. Nikos A.

palomo11 commented 4 years ago

OK. Thanks. I will do that, then.