BamBam

Description

bambam website  
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 PolyCat.

Environment Modules

Run module spider bambam to find out what environment modules are available for this application.

System Variables

• HPC_BAMBAM_DIR - installation directory
• HPC_BAMBAM_BIN - executable directory