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PLINK: ped2bed (version 2.0.0)
Allelic file in PED format
Map file

Ped to Bed format conversion is done with PLINK. Authors PLINK: Shaun Purcell (https://www.cog-genomics.org/plink)

Please cite "PLINK: a toolset for whole-genome association and population-based linkage analysis.", Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC., American Journal of Human Genetics, 81, 2007.
Please cite "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", Dereeper A. et al., Nucl. Acids Res. (1 july 2015) 43 (W1).

Galaxy integration Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)

Support For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr

Ped2Bed

Description

Ped to Bed format conversion is done with PLINK
PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
For further informations, please visit the PLINK website.

Dependencies

PLINK
plink 1.90b4, Conda version
Bioperl
perl-bioperl 1.6.924, Conda version

Input files

PED file

MAP file

Output files

Bed file

Fam file

Bim file

All logs

Working example

Input files

PED file

AZUCENA AZUCENA 0       0       0       0       G       G       A       A       C       C       T       T       T
BULUPANDAK      BULUPANDAK      0       0       0       0       G       G       A       A       A       A       T

MAP file

0       Chr1:4299       0       4299
0       Chr1:26710      0       26710
0       Chr1:56184      0       56184
0       Chr1:93272      0       93272

Output files

Bed file

binary file

Fam file

AZUCENA AZUCENA 0 0 0 -9
BULUPANDAK BULUPANDAK 0 0 0 -9

Bim file

0       Chr1:4299       0       4299    A       G
0       Chr8:18058      0       18058   C       T