Genotyping was performed on an Illumina Infinium iSelect Custom BeadChip. These arrays contain 340,000 attempted beadtypes for genotyping single nucleotide polymorphisms selected across the entire cat genome, using feline genome assembly felCat5. Of the 340,000 markers included on the array, 297,034 (87%) provided a reliable call.
SNPs for the array were selected from whole genome sequencing of 6 genetically diverse female DSH cats. These 6 cats were sequenced on a HiSeq2500 (Illumina, San Diego, CA) to generate 100 bp paired-end reads. Following GATK best practices pipeline (75 (link)), reads were mapped to the feline reference genome using BWA mem (76 (link)), then duplicate reads were tagged by PICARD MarkDuplicates, and indels were realigned and quality scores were recalibrated using GATK. Variants were called and filtered using GATK HaplotypeCaller and VCFtools (77 (link)). The full list of variants was thinned randomly using PLINK and then protein-coding variants with moderate and high impact as defined by SnpEff (78 (link)) were added back in.
SNPs for the array were selected from whole genome sequencing of 6 genetically diverse female DSH cats. These 6 cats were sequenced on a HiSeq2500 (Illumina, San Diego, CA) to generate 100 bp paired-end reads. Following GATK best practices pipeline (75 (link)), reads were mapped to the feline reference genome using BWA mem (76 (link)), then duplicate reads were tagged by PICARD MarkDuplicates, and indels were realigned and quality scores were recalibrated using GATK. Variants were called and filtered using GATK HaplotypeCaller and VCFtools (77 (link)). The full list of variants was thinned randomly using PLINK and then protein-coding variants with moderate and high impact as defined by SnpEff (78 (link)) were added back in.