Metadata-Version: 1.1
Name: vcf-annotate-polyphen
Version: 0.1.2
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
        ### As a library
        ```python
          import vap  # Vcf-Annotate-Polyphen (VAP)
        
          import sqlalchemy
          from sqlalchemy import create_engine
          engine = creative_engine('sqlite:///polyphen-2.2.2-whess-2011_12.sqlite')
          conn = engine.connect()
        
          annotation = vap.annotate_variant(conn, 'chr14', 20344588, 'C', 'A')
          print ("Gene: {}; Protein: {}; Change: {}; "
                   "HVar Prediction: {} (p: {}); HDiv Prediction: {} (p: {})") \
                   .format(
                    annotation.gene,
                    annotation.protein,
                    annotation.aa_change,
                    annotation.hvar_pred,
                    annotation.hvar_prob,
                    annotation.hdiv_pred,
                    annotation.hdiv_prob)
          # Gene: OR4K2; Protein: Q8NGD2; Change: H54Q;
          #  HVar Prediction: benign (p: 0.017); HDiv Prediction: benign (p: 0.008)
        ```
        
        ### Command line interface
        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:
        
        ```
        ...
        2	165351172	.	T	A	.	PASS	SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,.	GT:AD:BQ:DP:FA:SS	0:11,0:.:11:0.0:0	0/1:3,5:30.0:8:0.625:2
        2	179247908	.	C	G	.	PASS	SOMATIC;VT=SNP;PP2=OSBPL6,Q9BZF3,N593K,probably damaging,0.998,probably damaging,1.0	GT:AD:BQ:DP:FA:SS	0:27,2:.:29:0.069:0	0/1:27,4:28.0:31:0.129:2
        ...
        ```
        
        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 ./polyphen-2.2.2-whess-2011_12.sqlite ./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
