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By Sequencing"],"omics_type":["Genomics"],"submitter":["EMBL-EBI"],"instrument_platform":["-"],"species":["Sus Scrofa"],"full_dataset_link":["https://www.ebi.ac.uk/eva/?eva-study=PRJEB93975"],"repository":["EVA"],"additional_accession":[]},"is_claimable":false,"name":"Variant calling against pig reference genome (GCA_000003025.6) using pig strain reads","description":"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.","dates":{"publication":"2025-07-19"},"accession":"PRJEB93975","cross_references":{"TAXONOMY":["9823"]}}