Authors South Green
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
CheckGWASInputs checks concordance between input files for GWAS analysis.
Hapmap output
Trait output
Logfile and statistics
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
<Trait> Test Ind1 -2.9985936006411 Ind2 -2.68669426456267
rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2 Ind3 Ind4 SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA AA AA SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA AA TT
<Trait> Test Ind429 -26.2142525264157 Ind373 12.0306115988504 Ind81 1.98118654229534
============================================== Individuals ============================================== Individuals in hapmap file: 500 Individuals in trait file: 500 Individuals found in both files: 500 ============================================== Markers ============================================== Discarded markers: Monomorphic: 0 Not biallelic: 0 Modified markers: Difference in variation: 0