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.

Required Modules

Serial

• bambam

System Variables

• HPC_{{#uppercase:bambam}}_DIR - installation directory
• HPC_{{#uppercase:bambam}}_BIN - executable directory