Question: Unable to read large Vcf file in R
0
gravatar for sridevi
22 months ago by
sridevi0
sridevi0 wrote:

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: 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,

vcf files variantannotation R • 765 views
ADD COMMENTlink modified 22 months ago • written 22 months ago by sridevi0
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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.

ADD REPLYlink written 22 months ago by WouterDeCoster38k

why do you need

compressVcf<-bgzip(from,to)

if 'from' is already compressed ??

ADD REPLYlink written 22 months ago by Pierre Lindenbaum119k
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