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).
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).