hammerlab/vcf-annotate-polyphen

Name: vcf-annotate-polyphen

Owner: Hammer Lab

Description: A tool to annotate human VCF files with PolyPhen2 effect measures

Created: 2016-04-27 19:11:30.0

Updated: 2017-03-28 01:20:36.0

Pushed: 2016-05-03 16:00:10.0

Homepage: null

Size: 43

Language: Python

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README

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

p install vcf-annotate-polyphen

via Source Code

t checkout https://github.com/hammerlab/vcf-annotate-polyphen.git
 vcf-annotate-polyphen/
thon setup.py

Usage

As a library

port vap  # Vcf-Annotate-Polyphen (VAP)

port sqlalchemy
om sqlalchemy import create_engine
gine = create_engine('sqlite:///polyphen-2.2.2-whess-2011_12.sqlite')
nn = engine.connect()

notation = vap.annotate_variant(conn, 'chr14', 20344588, 'C', 'A')
int ("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:

f-annotate-polyphen --help
e: vcf-annotate-polyphen polyphen.whess.sqlite input.vcf output.vcf

ons:
, --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:

FO=<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:

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
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 usage

 example/
e following file is ~7 GB!!!
et "ftp://genetics.bwh.harvard.edu/pph2/whess/polyphen-2.2.2-whess-2011_12.sqlite.bz2"
nzip2 polyphen-2.2.2-whess-2011_12.sqlite.bz2
f-annotate-polyphen ./polyphen-2.2.2-whess-2011_12.sqlite ./TCGA-55-6543.vcf ./TCGA-55-6543.annotated.vcf
ss ./TCGA-55-6543.annotated.vcf