/bamsurgeon

tools for adding mutations to existing .bam files, used for testing mutation callers

Primary LanguagePythonMIT LicenseMIT

Bamsurgeon: tools for adding mutations to .bam files, used for testing mutation callers

Please see doc/Manual.pdf for instructions and contact adam.ewing@gmail.com with questions.

Prerequisites:

samtools/wgsim/tabix (https://github.com/samtools/samtools)
bcftools (https://github.com/samtools/bcftools)
pysam >= 0.8.1 (https://github.com/pysam-developers/pysam)
bwa (http://bio-bwa.sourceforge.net/)
velvet (http://www.ebi.ac.uk/~zerbino/velvet/)
exonerate (http://www.ebi.ac.uk/~guy/exonerate/)
picard tools >= 1.128 (https://github.com/broadinstitute/picard/releases/tag/1.128)