RAVE (version 1.0)

Select plink DB:

If your dataset of interest is not listed, contact us

Minor allele frequencies:

--maf filters out all variants with minor allele frequency below the provided threshold (default 0.01)

Filter SNP based on subpopulation:

Filter SNP based on individual (This parameter can be empty):

Variety list from file:

One range per line, whitespace-separated (i.e : B001 B001)

Filter SNP based on genomic location (This parameter can be empty):

Range list from file:

One range per line, whitespace-separated (i.e : 1 100000 120000 chr1)

Filter SNP based on specific locus (This parameter can be empty):

Locus file (MSU locus name):

One locus per line (i.e : LOC_Os01g13620)

Select output format:

--recode creates a new text fileset, after applying sample/variant filters and other operations.

Overview

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 https://ricediversity.org/data/

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

Support For any questions about Galaxy integration, please send an e-mail to southgreen@cirad.fr

Program encapsulated in Galaxy by South Green