dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.
shajoezhu
commented
3 years ago
./dEploid -vcf data/exampleData/PG0400-C.eg.vcf.gz -plaf data/exampleData/labStrains.eg.PLAF.txt -panel data/exampleData/labStrains.eg.panel.txt -o PG0400-C -seed 2 -exclude exclude.txt -best -nSample 500 -rate 8 -burn 0.67 -sigma 2.0 -vqslod 8
initialProp=$( cat PG0400-C.ibd.prop | tail -1 | sed -e "s/\t/ /g" )
./dEploid -vcf data/exampleData/PG0400-C.eg.vcf.gz -plaf data/exampleData/labStrains.eg.PLAF.txt -panel data/exampleData/labStrains.eg.panel.txt -exclude exclude.txt -o PG0400-C -initialP ${initialProp} -painting PG0400-C.final.hap