williarj/Boechera_Mutation_Accumulation
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A repository of programs used to analyze apomictic and sexual boechera genomes. Most all of these scripts have help info, if run with a -h option will give details on inputs needed. vcfSummarizer.py - takes a VCF file and a filter python script and creates a filtered and annotated SNP matrix filterBoechera.py - the filter file for use with vcfSummarizer filters SNPs based on genotype quality and proximity to called indels summary.py - a parser used to process snp matricies getRegions.py - used to create the 'pseudohaplotypes' takes a list of regions and a SNP matrix and produces haplotypes getHeterozygosity.py - takes a SNP matrix file and outputs windows of counts of called and heterozygous sites countTrees.py - counts the topologies of all the trees given in a list of trees countPairwiseDiversity.py - calculates pairwise differences between all samples in a SNP matrix countDerivedAlleles.py - counts, in windows, the number of derived alleles in a subsample of a SNP matrix. countSNPs.py - given a list of trees and their associated fasts this script counts the number of derived mutations on each branch of the trees.
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