GitHub - jpfeil/bamsurgeon: tools for adding mutations to existing .bam files, used for testing mutation callers

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

MIT license

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Name		Name	Last commit message	Last commit date
Latest commit History 290 Commits
bs		bs
doc		doc
etc		etc
test		test
test_data		test_data
Dockerfile		Dockerfile
LICENSE.txt		LICENSE.txt
README		README
addindel.py		addindel.py
addsnv.py		addsnv.py
addsv.py		addsv.py

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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)