In this article you will find information on the different types of configuration pipelines for the Swine species. The configuration include:
Swine low-pass v1.0
- Reference genome: susScr11
- Imputation reference panel: We used 414 samples from the publicly available swine sequence data (PRJEB39374, PRJNA343658, PRJNA414091, PRJNA482384, PRJNA506339, and PRJNA553106), and processed these data using GATK4 into a reference panel of 53M SNPs and short indels.
- Deliverables: original FASTQ, aligned BAM (and index), imputed VCF (and index)