asalomatov / anno-dbnsfp

anno-dbnsfp

Annotate non-synonymous SNPs with values found in dbNSFP.

Installation and usage for running on Simons Foundation/Flatiron Institute cluster.

sqlite3 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