https://github.com/simonsfoundation/anno-dbnsfp
https://github.com/simonsfoundation/anno-dbnsfp
Last synced: 2 months ago
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- Host: GitHub
- URL: https://github.com/simonsfoundation/anno-dbnsfp
- Owner: simonsfoundation
- License: mit
- Created: 2016-04-08T18:41:26.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2017-03-31T14:16:51.000Z (about 9 years ago)
- Last Synced: 2025-01-18T21:32:28.271Z (over 1 year ago)
- Language: Python
- Size: 15.6 KB
- Stars: 2
- Watchers: 4
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
## _anno-dbnsfp_
Annotate non-synonymous SNPs with values found in [dbNSFP](https://sites.google.com/site/jpopgen/dbNSFP).
### Installation and usage for running on Simons Foundation/Flatiron Institute cluster.
[sqlite3](http://www.sqlite.org/download.html) must be in your PATH.
```
pip install --user git+git://github.com/simonsfoundation/anno-dbnsfp.git
export PATH=$PATH:~/.local/bin
```
For help
```
anno-dbnsfp.py -h
```
Create an input file with mutations to be annotated.
```
echo 'CHROM,POS,ID,REF,ALT,GENE
13,23909440,.,G,A,SACS
21,35144452,.,G,A,ITSN1
1,180235688,.,G,A,LHX4
7,73731910,.,C,T,CLIP2
16,3820881,.,G,A,CREBBP
3,113508666,.,A,G,ATP6V1A
7,148512615,.,T,C,EZH2
11,8111646,.,A,C,TUB
3,21606142,.,G,T,ZNF385D
9,37015066,.,T,A,PAX5
2,223917672,.,G,A,KCNE4
16,71318883,.,T,C,CMTR2
18,21331038,.,A,G,LAMA3
17,78831603,.,G,A,RPTOR
12,49334805,.,A,G,RP11-302B13.5
5,145603023,.,C,T,RBM27
10,104596833,rs104894138,G,A,CYP17A1
12,120436359,.,G,A,CCDC64
1,213145953,.,C,T,VASH2' > test_mutations.csv
```
Annotate
```
anno-dbnsfp.py --genome_build=hg19 --input_delim=csv test_mutations.csv
cat test_mutations.csv.ann.tsv
```
To see all available dbNSFP columns
```
anno-dbnsfp.py -p test_mutations.csv
```