Authors Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform

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

HapmapToMLMMFiles

Description

HapmapToMLMMFiles converts a hapmap file into input files compatible with the MLMM software.

Dependencies

GAWK: gawk 4.1.3, Conda version

Input file

Hapmap file: Allelic file in Hapmap format

Output files

SNP Info file

Genotyping file for MLMM

Working example

Input files

Hapmap file

rs#     alleles chrom   pos     strand  assembly#       center  protLSID        assayLSID       panel   QCcode  Ind1    Ind2
SNP1    A/T     1       3102    +       assembly        NA      NA      NA      speciesname     NA      AA      AA      AA
SNP2    A/T     1       4648    +       assembly        NA      NA      NA      speciesname     NA      AA      AA      AA

Output files

SNP Info file

SNP     Chr     Pos
SNP1    1       3102
SNP2    1       4648
SNP3    1       7601

Genotyping file for MLMM

Ind_id  SNP1    SNP2    SNP3    SNP4    SNP5    SNP6    SNP7    SNP8    SNP9    SNP10   SNP11   SNP12   SNP13   SNP14
Ind1    0       0       0       0       0       0       2       0       2       0       0       0       2       0
Ind2    0       0       0       0       0       2       2       0       0       0       0       0       0       0