Difference between revisions of "BamBam"
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;PolyCat: see [http://udall-lab.byu.edu/Research/Software/PolyCat.aspx PolyCat]. | ;PolyCat: see [http://udall-lab.byu.edu/Research/Software/PolyCat.aspx PolyCat]. | ||
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Revision as of 14:01, 13 June 2022
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