I am running StrainFacts to identify strains of B. vulgatus in metagenomes. I am very happy with the results in that StrainFacts can recapitulate the results I found with StrainFinder, at least at the level of strain abundance (the community file). However, I am having difficulty interpreting the genotype file. This is how I extracted the genotype and the community file.
StrainFactsMetaGenome-fit.geno.tsv has a probability between 0 and 1 for the genotype for each strain at each position. My question is whether 0 or 1 corresponds to the Ref or the Alt in the input of metagenome SNP counts? My goal is to reconstruct a sequence for each one of these strains and insert it into a phylogenetic tree.
I am running StrainFacts to identify strains of B. vulgatus in metagenomes. I am very happy with the results in that StrainFacts can recapitulate the results I found with StrainFinder, at least at the level of strain abundance (the community file). However, I am having difficulty interpreting the genotype file. This is how I extracted the genotype and the community file.
sfacts dump ../Results/StrainFactsMetaGenome-fit.nc --genotype StrainFactsMetaGenome-fit.geno.tsv --community StrainFactsMetaGenome-fit.comm.tsv
StrainFactsMetaGenome-fit.geno.tsv has a probability between 0 and 1 for the genotype for each strain at each position. My question is whether 0 or 1 corresponds to the Ref or the Alt in the input of metagenome SNP counts? My goal is to reconstruct a sequence for each one of these strains and insert it into a phylogenetic tree.