Comments (3)
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.
from clinvar.
Thanks, it works fine now with older data...
from clinvar.
#21 from @XiaoleiZ has fixed parsing for the new datafiles, so we're back to making up-to-date releases.
from clinvar.
Related Issues (20)
- Sometimes "symbol" disagrees with primary hgvs gene annotation HOT 1
- Missing variants HOT 4
- RScript crash HOT 1
- Feature request: Including strand info and genomic start and end coordinates HOT 1
- Wrong gene mapping HOT 2
- Add "last_evaluated" field to VCF
- Improper handling of pseudoautosomal region HOT 1
- Improper labelling of conflicting variants as pathogenic HOT 3
- Job parse failure on system execution. ENV issues? HOT 5
- Another translation for gold stars
- Add LICENSE HOT 2
- Need to Update pathogenic & conflict boolean regex. HOT 1
- ClinSig changes for some halpotypes in join_data.R - become wrong! HOT 2
- Clinical Significance Order Lost in Allele Grouping HOT 8
- Convert the pipeline to hail for .tsv processing steps?
- Augmented tables in output HOT 2
- missing clinvar_alleles_with_exac_v1.*.tsv.gz HOT 1
- Mismatch between clinical_significance_ordered and submitters_ordered HOT 2
- Multiple isoforms not in index
- missing hgvs_c when indel is realigned and shifted.
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from clinvar.