Supplemental Material for Falker-Gieske et al., 2019
datasetposted on 11.07.2019 by Clemens Falker-Gieske, Iulia Blaj, Siegfried Preuß, Jörn Bennewitz, Georg Thaller, Jens Tetens
Datasets usually provide raw data for analysis. This raw data often comes in spreadsheet form, but can be any collection of data, on which analysis can be performed.
Supplementary Table 1 contains the coefficients of determination (R²) for each variant on QTL harboring chromosomes where calculation was possible. Supplementary Table 2 containts the complete list of clusters identified in the GWAS with additional supporting information for cluster assignment. GRMs from F2 60k genotypes (File_S1.zip) were created by a "leave one chromsome out" approach using the program "Genome-wide Complex Trait Analysis (GCTA) version 1.91.4 beta3".GWAS was conducted with imputed sequence level F2 genotypes (Supplementary File_S2.zip) for each chromosome using the GRM where the respective chromosome was left out(GRM command: gcta64 --bfile SG_F2_chip_wo_chrNO --autosome --maf 0.01 --make-grm --out SG_F2_chip_wo_chrNO --thread-num 10 --autosome-num 18 ; GWAS command: gcta64 --mlma --covar Kiel_Hoh_cross.covar --bfile F2_beagle4.0_ped_ChrNO --grm SG_F2_chip_wo_chrNO --pheno TRAIT.pheno --out TRAIT_chrNO --maf 0.01 --thread-num 10; replace NO with the respective chromosome number and TRAIT with the respective trait to be analyzed) Phenotype files located in Supplementary File_S2.zip for the traits ADG, BFT, MFR, and CRCL were used in the GWAS. Crosses were used as covariates in the GWAS and provided as a gcta compatible covar file in Supplemental File_S4.zip. SNP locations can be found in the bim files of the genotype data (Supplementary File_S1.zip and Supplementary File_S2.zip). Population structure information is provided in form of a Beagle 4.0 compatible pedigree file (Supplementary File_S3.zip). Raw sequencing data will be made publicly available in the NCBI Sequence Read Archive (SRA). File_S5 contains the 60k chip genotype data in variant call file (VCF) format. Genomic positions have been lifted to genome assembly Sus scrofa 11.1 (GCA_000003025.6) and annotated with dbSNP build 150. gcta compatible covar files for the conditional association analyses with top variants are provided in File_S6.