Fig. 6
Workflow diagram to compare SNP calling approaches, identify functional SNP, and predict corresponding variant effects. i Samples were merged based on three different approaches: i) Non-merged samples, meaning BAM files were not merged and each file was called individually using a multi-sample VCF file containing 6 GT (1 for each animal) for each group; ii) Merged samples for low-RFI and merged samples for high-RFI for each tissue, meaning BAM files of same group and tissue were merged. Using one VCF file for each RFI group per tissue, containing 1 GT; iii) Merged samples for low- and high-RFI for both tissues, meaning BAM files of same group were merged for tissues. Using one VCF file for each RFI group for both tissues, containing 1 GT. RFI = residual feed intake; GT = genotype; SNP = single nucleotide polymorphism; VCF = variant calling format