BamBam includes numerous tools for analyzing DNA next-generation sequencing data. Tools are provided for calling SNPs and indels, identifying large scale deletions, tabulating counts of mapped reads, methylation analysis, and more.
Depends on SAMtools (http://samtools.sourceforge.net/) and BAMtools (https://github.com/pezmaster31/bamtools). Also uses BioPerl, which is included in the download tarball.
- call SNPs and indels
- impute genotypes
- build consensus sequences
- tabulate counts of mapped reads (RNA-seq)
- infer haplotype phasing with K-means clustering
- analyze DNA methylation (bisulfite-sequencing)
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