Entering edit mode
7.9 years ago
Alexander Skates ▴ 370
Hi, I'm trying to read a VCF file I have using readVcf, however the following occurs:
fl <- file.path('tmp', 'vcf', 'rs11780156.genotypes.vcf.gz') vcf <- readVcf(fl, 'hg19') scanVcfHeader(fl) class: VCFHeader samples(190): HG00096 HG00097 ... NA12889 NA12890 meta(2): META contig fixed(2): FILTER ALT info(27): CIEND CIPOS ... EX_TARGET MULTI_ALLELIC geno(0): > dim(vcf)  13161 0 > geno(vcf) List of length 0 names(0):
I've looked at the file itself, and it definitely has the sample genotypes in it, so I'm not sure why geno(vcf) is empty.
The file in question is at https://www.dropbox.com/s/qwa0xoaksnnyev4s/rs11780156.genotypes.vcf.gz?dl=0 however it seems to apply to any that I try and load via readVcf. These are just VCF I files I downloaded from 1000 Genomes using tabix.
Sorry, broken link: https://www.dropbox.com/s/qwa0xoaksnnye4s/rs11780156.genotypes.vcf.gz?dl=0
Please paste output of
sessionInfo(), gonna guess that you are missing a parameter in the read
Hi Ying, it turned out that the issue was 1000 Genomes (the original source for the data) were missing the FORMAT lines in the header. I got in touch with them and they fixed it, so this is no longer an issue.