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RAVE (version 1.0)
If your dataset of interest is not listed, contact us
--maf filters out all variants with minor allele frequency below the provided threshold (default 0.01)
One range per line, whitespace-separated (i.e : B001 B001)
One range per line, whitespace-separated (i.e : 1 100000 120000 chr1)
One locus per line (i.e : LOC_Os01g13620)
--recode creates a new text fileset, after applying sample/variant filters and other operations.


PLINK Overview

PLINK2 Majority of information in this page is derived from an excellent PLINK manual written by Shaun Purcell, Christopher Chang.

Input formats

Plink binary file (bed/bim/fam)

Example : Plink binary for High Density Rice Array (HDRA, 700k SNPs, McCouch SR et al. Nat Commun 7, 10532)

See Plink genotype data bundle available at

Galaxy integration Droc Gaetan (CIRAD), Ruiz Manuel (CIRAD).

Support For any questions about Galaxy integration, please send an e-mail to

Program encapsulated in Galaxy by South Green