User: askates

gravatar for askates
askates10
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New User
Location:
United Kingdom
Last seen:
4 years, 6 months ago
Joined:
4 years, 6 months ago
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a***************@googlemail.com

Posts by askates

<prev • 5 results • page 1 of 1 • next >
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Comment: 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 4.5 years ago by askates10
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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 4.5 years ago by askates10
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Comment: 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 4.5 years ago by askates10
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Comment: 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 4.5 years ago by askates10
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ReadVCF not reading samples
... 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 ...
variantannotation vcf readvcf written 4.6 years ago by askates10

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Popular Question 4.5 years ago, created a question with more than 1,000 views. For ReadVCF not reading samples

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