User: askates
askates • 10
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- United Kingdom
- Last seen:
- 4 years, 4 months ago
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- 4 years, 5 months ago
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Posts by askates
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C: ReadVCF not reading samples
... I got in touch with 1000 Genomes, and they have now resolved the issue on their end. Thanks for all your help, Valerie.
...
written 4.4 years ago by
askates • 10
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Comment:
C: ReadVCF not reading samples
... I did download subsets through tabix, and it seemed to work -- the fact that I get the issue when I reference the file directly from their ftp leads me to believe that the issue is on their end though. See above:
> fl2 <- "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr1.ph ...
written 4.4 years ago by
askates • 10
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C: ReadVCF not reading samples
... Thanks Valerie, you're a life saver! Is there any way to parse the data without explicitly altering the physical files, for example by loading it into a TabixFile and altering it there? Otherwise it would mean downloading all 1000 Genomes chromosomes to disk, in total about ~16 GB, and I'd like to a ...
written 4.4 years ago by
askates • 10
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C: ReadVCF not reading samples
... Sorry, not sure what happened with the link. https://www.dropbox.com/s/qwa0xoaksnnye4s/rs11780156.genotypes.vcf.gz?dl=0 should hopefully work!
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS
locale:
[1] LC_CTYPE=en_GB.UTF-8 ...
written 4.4 years ago by
askates • 10
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... 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 cont ...
written 4.4 years ago by
askates • 10
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