ReadVCF not reading samples

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9.5 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)
[1] 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.

readVcf VariantAnnotation R • 3.2k views

ADD COMMENT • link updated 22 months ago by Ram 44k • written 9.5 years ago by Alexander Skates ▴ 370

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Sorry, broken link: https://www.dropbox.com/s/qwa0xoaksnnye4s/rs11780156.genotypes.vcf.gz?dl=0

ADD REPLY • link updated 22 months ago by Ram 44k • written 9.5 years ago by Alexander Skates ▴ 370

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Please paste output of sessionInfo(), gonna guess that you are missing a parameter in the read

ADD REPLY • link updated 22 months ago by Ram 44k • written 9.5 years ago by Ying W ★ 4.3k

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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.

ADD REPLY • link 9.5 years ago by Alexander Skates ▴ 370

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