Can be done on output of Pipeline_GBLUP by modifing the column names or before doing GWAS by GBLUP by modifiying the file phenotypes
GWAS by GBLUP ~ 24h for multivariate analysis
Pipeline_GATK : All pink/purple scripts can be found in
Isotypes : All orange scripts can be found in
Heterozigosity : All light green scripts can be found in
Plot_stat_vcf.R mentionned in dark green box can be found in Plots
Imputation : All red script can be found in
Pipeline_GBLUP : All light blue script can be found in
G-matrix : All dark blue script can be found in
DataAnalysing : All script to analyse bam file quality, and number of lines belonging to each population
All folder has a README file
Some of them has an ARCHIVES file, which indicates where input/output files are stored on lab computers
pdf results and other minor outputs can be found on GEVPC10 on /mnt/data2/desmarais/ in Àrchive.zip