Just wanted to check if anyone else is having issues downloading the VCF files from the FTP source for Clinvar.
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/
This is the error I'm running into
550 /pub/clinvar/vcf_GRCh37: No such file or directory
Looks the directory is missing since the last update.
Any other alternate sources to get this from? I also observed that the web version has a lot more variants per gene than the version offered for download from the previous release. I hope this will be fixed in the current release.
2 answers
The dbSNP site has the clinvar VCF (and has for a while).
ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/
As of today, the header contains the following metadata:
#fileformat=VCFv4.0
##fileDate=20141009
##source=ClinVar and dbSNP
##dbSNP_BUILD_ID=142
##reference=GRCh38
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Sean Davis
Depending upon your application, you may be able to use tools like ANNOVAR (or ANNOVAR's database file) to get the relevant ClinVar stats:
http://www.openbioinformatics.org/annovar/annovar_filter.html#clinvar
I personally haven't tried to define the ClinVar variants from scratch
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Charles Warden
Yes I did see that. However like I mentioned there is a difference in number of variants available from the web version and the previous download release. For example the gene CYP27A1 has 67 pathogenic variants from the web query
http://www.ncbi.nlm.nih.gov/clinvar/?term=CYP27A1
However only 15 show up in the FTP release. I was hoping the latest release from earlier this month would have fixed that.
Yeah, there might be some sort of delay. You could try contacting somebody from NCBI to see if they can help (or at least confirm that the newer annotations are not currently available from the FTP):
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Charles Warden
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Don't feel too aggrieved, the vcf_GRC38 link is broken too.