[R-sig-genetics] Reading large VCF into genind

[Sven E. Templer]

Dear Stefano,

could you describe which package:::function(s) you used (providing code
helps to help!)?

You could split the vcf file before reading it into the R workspace by
chromosomes (use GNU grep, for example), then extract data for single files
(e.g. frequencies, subset of SNPs, etc.). Export this data, and start a new
session which loads only the processed information.

Best,
Sven



On 29 May 2015 at 16:07, Stefano Iantorno <si3 at sanger.ac.uk> wrote:

> Hello
>
> I have a VCF file containing 306596 biallelic SNP calls from 18
> individuals. I was able to read the entire file as a “loci” object but when
> I try to convert it into a genind object I run into memory issues.
>
> How can I circumvent this problem? Should I break the single “loci” object
> into smaller subsets with only 50 000 SNPs or so, and convert each one into
> a genind object separately with loci2genind? How do I combine the resulting
> genind objects?
>
> - Stefano
>
>
>
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