Skip to main content

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 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
```

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for vcf-annotate-polyphen, version 0.1.2
Filename, size File type Python version Upload date Hashes
Filename, size vcf-annotate-polyphen-0.1.2.tar.gz (16.3 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page