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Unable to read large Vcf file in R

Hi,

Is there any way to read large vector VCF files in R . The below doesn't seem to work, where as it works for small vcf files.

vcf21<-read.vcfR("D:\\ALL.chr21.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz",verbose = FALSE)

Error in read.vcfR("D:\\ALL.chr21.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz",  : 
  negative length vectors are not allowed

Thanks in Advance

variantannotation r vcf
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updated by Ram Ram • written by sridevi • sridevi

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

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The below doesn't seem to work

Does it give an error? What makes you think it doesn't work? Please be as informative as possible.

• 0 views • link
written by WouterDeCoster WouterDeCoster

why do you need

compressVcf<-bgzip(from,to)

if 'from' is already compressed ??

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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