Generate a report based on the ClinVar variant database.
This code is a slightly modified and stand alone version of the report generation from the Genevieve project.
You'll need a local copy of the clinvar.vcf file from ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar.vcf.gz .
You can either download this yourself or run the setup.sh script provided.
$ ./setup.sh
********************************************************************************
This script will now download the latest clinvar.vcf.gz data, decompress it,
and put it in the data/ directory....
********************************************************************************
...
Fetching the latest clinvar.vcf.gz file from ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar.vcf.gz
...
decompressing...
...
********************************************************************************
Assuming the clinvar.vcf file is downloaded and ready, you can generate a test
report on the sample data provided by issuing the following command:
./src/clinvar_report.py -C data/clinvar.vcf -i data/abe.vcf
********************************************************************************
A sample VCF file is provided, abe.vcf, that you can do a test run on:
$ ./src/clinvar_report.py -C data/clinvar.vcf -i data/abe.vcf
Which will produce output like the following:
Chromosome,Position,Name,Significance,Frequency,Zygosity,ACC URL
1,45444038,not_specified,other,0.2965,Het,http://www.ncbi.nlm.nih.gov/clinvar/RCV000081999.4
1,46660295,not_specified,other,0.3335,Het,http://www.ncbi.nlm.nih.gov/clinvar/RCV000081805.4
1,46870761,Drug_addiction\x2c_susceptibility_to,other,0.2616,Het,http://www.ncbi.nlm.nih.gov/clinvar/RCV000007116.2
1,70904800,Homocysteine\x2c_total_plasma\x2c_elevated,pathogenic,0.2053,Het,http://www.ncbi.nlm.nih.gov/clinvar/RCV000003075.1
1,154426970,Serum_level_of_interleukin-6_soluble_receptor,other,0.2931,Het,http://www.ncbi.nlm.nih.gov/clinvar/RCV000015767.1
1,156105028,not_specified,other,0.1931,Het,http://www.ncbi.nlm.nih.gov/clinvar/RCV000041374.5
1,156106185,not_specified,other,0.2492,Het,http://www.ncbi.nlm.nih.gov/clinvar/RCV000041315.5
1,156107534,not_specified,other,0.2202,Het,http://www.ncbi.nlm.nih.gov/clinvar/RCV000041327.4
1,161009523,Hyperlipidemia\x2c_familial_combined\x2c_susceptibility_to,other,0.1703,Het,http://www.ncbi.nlm.nih.gov/clinvar/RCV000013088.1
...
See the LICENSE.txt for details. The VCF file, abe.vcf (and abe-sample-report.json) are provided under a CC0 license.
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