VariantAnnotation: error from readVcf command
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6.2 years ago
pifferdavide ▴ 100

I installed the package VariantAnnotation.I followed instructions to run the readVcf command: http://www.bioconductor.org/packages/release/bioc/vignettes/VariantAnnotation/inst/doc/VariantAnnotation.pdf

I set the working directory to the folder containing the vcf file and ran the following code. I guess it is telling me that my RAM memory (8gb) is too small to open Chr1?

> library(VariantAnnotation)
> fl <-  ("ALL.chr1.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf ")
> vcf <- readVcf(fl, "hg19")
Error: scanVcf: 'Realloc' could not re-allocate memory (5128192000 bytes)
  path: C:\Users\Davide\vcf1\ALL.chr1.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf
In addition: Warning messages:
1: In doTryCatch(return(expr), name, parentenv, handler) :
  Reached total allocation of 8077Mb: see help(memory.size)
2: In doTryCatch(return(expr), name, parentenv, handler) :
  Reached total allocation of 8077Mb: see help(memory.size)

R VariantAnnotation • 2.2k views
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