Usage

reports 1 or more consensus sequences for each BAM file provided

extracts and summarizes methylation values from a BAM file prepared by MethHead

summarizes the number of reads mapped to each annotated feature, 1 column per BAM

takes 2 BAM files and reports ranges where one of the BAMs has nothing and the other has something

infers haplotypes from a set of BAM files based on K-means clustering

takes 1 or more BAM files and writes out a ".snp" file with a summary of all polymorphic loci

converts a BAM file with bisulfite-treated reads in 4 possible orientations to one with only 2 possible orientations (for use with CalcMeth)

changes the coordinates in a BAM file as if it had been built from a different reference sequence

infers phylogenetic tree using MCMC

pipeline for mapping and categorizing next-generation sequence data from allopolyploid organisms