Question

how to import/read .vcf files in R

1

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anamarija ▴ 10

@anamarija-22787

Last seen 3.8 years ago

Hello,

I tried doing:

> library(vcfR)
> vcf <- read.vcfR("ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf", verbose = FALSE )

but this takes forever to load and I am not sure it is even working.

Any other suggestion on how I can read in .vcf file in R?

I intend to create covariance matrix file from this data.

Thanks

vcf • 5.7k views

ADD COMMENT • link 4.3 years ago anamarija ▴ 10

score 1 · Answer 1 · 2020-01-28

1

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Martin Morgan 25k

@martin-morgan-1513

Last seen 13 days ago

United States

The relevant Bioconductor packages might include VariantAnnotation and VariantFiltering depending on use case, which it would be helpful for you to present. If the VCF file is large (sounds like it is) then you'll either want to process the file by iterating through it, or by querying for ranges of interest (using VcfParam()). Both of these approaches are discussed in the VariantAnnotation vignettes here and here.

ADD COMMENT • link 4.3 years ago Martin Morgan 25k

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Hi,

thanks for getting back to me. I intend to create covariance matrix file but I also have to account for population and relatedness in files which I downloaded from here: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/. Taken that in account which software you would use for this purpose?

ADD REPLY • link 4.3 years ago anamarija ▴ 10