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README.md

Scripts and tutorials for using dbSNP data

dbSNP build release JSON files are available on the FTP site (ftp://ftp.ncbi.nih.gov/snp/latest_release/JSON).

directory layout

.
├── Variation Services                   # Tutorial for working with SPDI Variation Service
├── eUtils.ipynb                         # Sample dbSNP eUtils query 
├── extract_flank.sh                     # Script using eUtils to get rs flanking sequences 
├── MafGraph.ipynb                       # eUtils query and MAF parsing and graphing
├── hadoop_json_annotation.py            # parse dbSNP RS JSON object and extract the rs annotation using Hadoop
├── hadoop_json_clinical.py              # parse dbSNP RS JSON object and extract clinical rs data using Hadoop
├── hadoop_json_merge.py                 # parse dbSNP RS JSON object and extract rs merge history using Hadoop
├── hadoop_json_placement.py             # parse dbSNP RS JSON object and extract rs mapping information (ie. position)
├── refsnp-sample.json.gz                # Sample data containing one RefSNP JSON example for rs268 for testing             rsjson_demo.py  
├── rsjson_demo.py                       # Sample Python script to parse RefSNP (rs) JSON object.   The script
|                                          produces a tab-delimited output containing the assembly version, sequence ID, 
|                                          position, reference allele, variant allele and ClinVar clinical significance, 
|                                          if available. NOTE: this script was tested using Python 2.7.12.
├── rsjson_allele_info_demo.py           # Extract allele information  position, mrna and protein SPDI reference allele (inserted) and variant (deleted) sequence
├── rsjson_getss_info_demo.py            # Extract submission information (ss, local_snp_id, etc.)

└── README.md

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Notebook Description Binder
eUtils.ipynb dbSNP eUtils query Binder
MafGraph.ipynb eUtils query and MAF parsing and graphing Binder
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