Read processing and alignment. A pipeline adapted from the Genome Analysis Toolkit (GATK) (59) Best Practices Guide was used to process raw reads before genotype calling. Briefly, paired-end raw sequence reads, 150 bases in length, were aligned to the domestic dog reference genome, canFam3.1, using BWA-MEM (60) before the removal of polymerase chain reaction duplicates and low-quality reads. Lacking a database of known variants, the bootstrapping method of base quality score recalibration as recommended by GATK was performed by calling raw genotypes with GATK UnifiedGenotyper (minimum base quality Phred score of 20) and using these variants as input for recalibration with BaseRecalibrator. This process was repeated three times to reach convergence between reported and empirical quality scores. The full pipeline used for read processing and alignment, with example commands, is available at https://doi.org/10.5281/zenodo.2666099.

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