View source for BamBam

[[Category:Software]][[Category:Biology]][[Category:Genomics]]
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|{{#vardefine:url|http://udall-lab.byu.edu/Research/Software/BamBam.aspx}}
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BamBam - several simple-to-use tools to facilitate NGS analysis

BamBam's goal is to be useful and easy-to-use. The tools in this package try to do things in the simplest way possible and avoid, as much as possible, any special formats. Where a special format is needed, there's a program or script that generates that file format. Run any program or script without arguments to see command-line usage information. 
===Tools===

;Bam2Consensus: reports 1 or more consensus sequences for each BAM file provided
;CalcMeth: extracts and summarizes methylation values from a BAM file prepared by MethHead
;Counter: summarizes the number of reads mapped to each annotated feature, 1 column per BAM
;Gapfall: takes 2 BAM files and reports ranges where one of the BAMs has nothing and the other has something
;HapHunt: infers haplotypes from a set of BAM files based on K-means clustering
;InterSnp: takes 1 or more BAM files and writes out a ".snp" file with a summary of all polymorphic loci
;MethHead: converts a BAM file with bisulfite-treated reads in 4 possible orientations to one with only 2 possible orientations (for use with CalcMeth)
;ModRef: changes the coordinates in a BAM file as if it had been built from a different reference sequence
;Pebbles: infers phylogenetic tree using MCMC
;PolyCat: see [http://udall-lab.byu.edu/Research/Software/PolyCat.aspx PolyCat].
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