Update the script to parse the latest ClinVar 2017 May XML release and the resulting output files. The variant_summary.txt file from ClinVar has missing values and are different from ClinVar webpage. Thus the old version txt file is used (201703). To run this pipeline with old version txt file:
bw2
commented
7 years ago
Update the script to parse the latest ClinVar 2017 May XML release and the resulting output files. The variant_summary.txt file from ClinVar has missing values and are different from ClinVar webpage. Thus the old version txt file is used (201703). To run this pipeline with old version txt file:
python2.7 master.py --b37-genome /path/to/b37.fa --b38-genome /path/to/b38.fa -E /path/to/ExAC.r1.sites.vep.vcf.gz -S /path/to/variant_summary_2017-03.txt.gz -GG /path/to/gnomad.genomes.r2.0.1.sites.coding.autosomes_and_X.vcf.gz -GE /path/to/gnomad.exomes.r2.0.1.sites.vcf.gz
I also add a limitation part in README.md to explain the issue.