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_BAMBAM_DIR - installation directory
HPC_BAMBAM_BIN - executable directory

Validation

Validated 4/5/2018

BamBam