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Table 1 The core independent tools of BamBam

From: BamBam: genome sequence analysis tools for biologists

Section

Tool

Purpose

Single nucleotide Polymorphisms

InterSnp

Call SNPs between two or more samples

 

Pebbles

Impute genotypes in output from InterSnp

 

HapHunt

Phase haplotypes with K-means

Copy number Variants

GapFall

Identify deletions between two samples

 

Elfen

Identify covered regions

 

HMMph

Call copy number variants with HMM

Bisulfite-sequence Analysis

MetHead

Summarize base pair methylation in bisulfite-sequence data

GeneVisitor

Bam2Consensus

Generate consensus sequences from one or more samples

 

Bam2Fastq

Extract mapped and unmapped reads from BAM files

 

Counter

Summarize read coverage of sequences or regions

 

SubBam

Extract subset of mapped reads

Allopolyploid analysis

PolyCat

Categorize reads by genome based on similarity to parents

Scripts

Various

Various