BamBam

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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