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
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
```
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
```
