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a tool to annotate human VCF files with PolyPhen2 effect measures

Project 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
$ cd vcf-annotate-polyphen/
$ python

## Usage
### As a library
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: {})") \
# 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

-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]( 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 ""
$ 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

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