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

[Stefano Iantorno]

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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