Variant calling against pig reference genome (GCA_000003025.6) using pig strain reads

We ran nf-core/sarek pipeline using 297 paired-end reads from 130 samples from 15 different pig strains. 5 callers were utilised - strelka, deepvariant, freebayes, haplotypecaller, and mpileup. Variants were retained if called by at least 3 callers. The genotyping was done on strelka and deepvariant gVCF output using illumina gvcfgenotyper and GLnexus respectively. The best genotype is retained based on genotype quality. The pipeline generated ~15 million novel variants that would enrich variant deserts on the pig reference genome.