Metadata-Version: 1.1
Name: vcf-annotate-polyphen
Version: 0.1.1
Summary: a tool to annotate human VCF files with PolyPhen2 effect measures
Home-page: https://github.com/hammerlab/vcf-annotate-polyphen
Author: B. Arman Aksoy
Author-email: arman@aksoy.org
License: http://www.apache.org/licenses/LICENSE-2.0.html
Description: # vcf-annotate-polyphen
        A tool to annotate human VCF files with PolyPhen-2 effect measures.
        This tool only works on human variants,
        collects ClinVar scores,
        and assumes the VCF follows `hg19/GRCh37` conventions.
        
        ## Install
        ### via PyPi
        ```
        $ pip install vcf-annotate-polyphen
        ```
        
        ### via Source Code
        ```
        $ git checkout https://github.com/hammerlab/vcf-annotate-polyphen.git
        $ cd vcf-annotate-polyphen/
        $ python setup.py
        ```
        
        ## Usage
        After installing the package, you can invoke the command line utility as follows:
        
        ```
        $ vcf-annotate-polyphen --help
        Usage: vcf-annotate-polyphen polyphen.whess.sqlite input.vcf output.vcf
        
        Options:
          -h, --help  show this help message and exit
        ```
        
        As listed above in the help text, this tool expects three arguments from the user:
        
        1. [PolyPhen-2 WHESS](ftp://genetics.bwh.harvard.edu/pph2/whess) in SQLite format
        2. Input VCF to be annotated
        3. Output VCF to be written with annotations
        
        The output file should have an additional `INFO` field as described below:
        
        ```
        ##INFO=<ID=PP2,Number=1,Type=String,Description="PolyPhen2 annotations in the following order:Gene name; UniProt id; Amino acid change; ClinVar effect category; Strength of effect (probability)">
        ```
        
        which manifests itself for each variant description:
        
        ```
        ...
        #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  SAMPLE
        2       165351172       .       T       A       .       PASS    SOMATIC;VT=SNP;PP2=.,.,.,.,.    GT:AD:BQ:DP:FA:SS       0:11,0:.:11:0.0:0       0/1:3,5:30.0:8:0.625:22       179247908       .       C       G       .       PASS    SOMATIC;VT=SNP;PP2=OSBPL6,Q9BZF3,N593K,probably damaging,0.998  GT:AD:BQ:DP:FA:SS       0:27,2:.:29:0.069:0     0/1:27,4:28.0:31:0.129:2
        7       99796940        .       G       A       .       PASS    SOMATIC;VT=SNP;PP2=STAG3,Q9UJ98,R508Q,benign,0.0        GT:AD:BQ:DP:FA:SS       0:37,0:.:37:0.0:0       0/1:49,10:30.0:59:0.169:2
        ...
        ```
        
        Here is an annotated VCF: [example/TCGA-55-6543.annotated.vcf](example/TCGA-55-6543.annotated.vcf).
        
        ### Example usage
        ```
        $ cd example/
        # The following file is ~7 GB!!!
        $ wget "ftp://genetics.bwh.harvard.edu/pph2/whess/polyphen-2.2.2-whess-2011_12.sqlite.bz2"
        $ bunzip2 polyphen-2.2.2-whess-2011_12.sqlite.bz2
        $ vcf-annotate-polyphen ./TCGA-55-6543.vcf ./TCGA-55-6543.annotated.vcf
        $ less ./TCGA-55-6543.annotated.vcf
        ```
        
Keywords: vcf-annotate-polyphen
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: ISC License (ISCL)
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
