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        "author": "Ino de Bruijn",
        "author_email": "ino@ino.pm",
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            "Development Status :: 2 - Pre-Alpha",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Natural Language :: English",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.6",
            "Programming Language :: Python :: 2.7",
            "Topic :: Software Development :: Libraries :: Python Modules"
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        "description": "So U Found A Mutation? (SUFAM)\n==============================\n.. image:: https://badge.fury.io/py/sufam.svg\n    :target: http://badge.fury.io/py/sufam\n.. image:: http://anaconda.org/inodb/sufam/badges/version.svg\n    :target: http://anaconda.org/inodb/sufam\n.. image:: https://travis-ci.org/inodb/sufam.svg?branch=master\n    :target: https://travis-ci.org/inodb/sufam\n\nFound a mutation in one or more samples? Now you want to check if they are in\nanother sample. Unfortunately mutect, varscan or whatever other variant caller\nis not calling them. Use SUFAM. The super sensitive validation caller that\ncalls everything on a given position. All you need is a vcf with the mutations\nthat you are interested in and the sam/bam file of the sample where you want to\nfind the same inconsipicuous mutation.\n\nInstallation\n------------\n::\n\n    pip install sufam\n\nRun\n---\n::\n\n    usage: sufam [-h] [--sample_name SAMPLE_NAME] [--format {matrix,sufam}]\n                [--mpileup-parameters MPILEUP_PARAMETERS] [--version]\n                reffa vcf bam\n\n    So U Found A Mutation? (SUFAM)\n\n    Found a mutation in one or more samples? Now you want to check if they are in\n    another sample. Unfortunately mutect, varscan or whatever other variant caller\n    is not calling them. Use SUFAM. The super sensitive validation caller that\n    calls everything on a given position. All you need is a vcf with the mutations\n    that you are interested in and the sam/bam file of the sample where you want to\n    find the same inconsipicuous mutation.\n\n    Author: inodb\n\n    positional arguments:\n    reffa                 Reference genome (fasta)\n    vcf                   VCF with mutations to be validated\n    bam                   BAM to find mutations in\n\n    optional arguments:\n    -h, --help            show this help message and exit\n    --sample_name SAMPLE_NAME\n                            Set name of sample, used in output [name of bam].\n    --format {matrix,sufam}\n                            Set output format [sufam]\n    --mpileup-parameters MPILEUP_PARAMETERS\n                            Set options for mpileup [--ignore-RG --min-MQ 1 --max-\n                            depth 250000 --max-idepth 250000]\n    --version             show program's version number and exit\n\nExample\n~~~~~~~\nVCF file like::\n\n    #CHROM\tPOS\tID\tREF\tALT\n    17\t7574012\tCOSM11286,COSM214290\tC\tG\n    17\t7574012\tCOSM11286,COSM214290\tC\tA\n\nCheck if given mutations are in a bam file::\n\n    sufam human_g1k_v37_chr17.fa mutations.vcf subset1.bam 2> example/sufam.log > example/sufam.tsv\n\nOutput:\n\n- `example/sufam.log <example/sufam.log>`_\n- `example/sufam.tsv <example/sufam.tsv>`_\n \nDevelopers\n----------\nTests\n~~~~~\nIn root dir run::\n\n    nosetests\n\nFor individual tests::\n\n    nosetests -s tests/test_validation.py:TestValidation.test_validate_mutations_indel",
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