Issue with R script about clinvar

[kristjaneerik]

I believe this is the error I was seeing with the latest update from ClinVar at #18. The R script tries to select columns from the variant summary table that are not there (but used to be).

There is currently no fix, other than to use older ClinVar data.
For this download the ClinVar XML and variant summary table.
Then run e.g.:

python master.py \
    -R <hg19.fa> \
    -E ExAC.r0.3.1.sites.vep.vcf.gz \
    -X ClinVarFullRelease_2016-09.xml.gz \
    -S variant_summary_2016-09.txt.gz

The R script is broken with data from 2016-10 onward it seems.

[VivekTodur]

Thanks, it works fine now with older data...

[bw2]

#21 from @XiaoleiZ has fixed parsing for the new datafiles, so we're back to making up-to-date releases.