In this article you will find information on the different types of configuration pipelines for the Chicken species. The configuration include:
Chicken low-pass v1.0
- Reference genome: galGal6
- Imputation reference panel: Sequencing data was downloaded from the European Nucleotide Archive project PRJEB30270. These data are described in detail in Qanbari et al. (2019). Raw sequences were processed using GATK4 and 26M variants were identified and converted into a haplotype reference panel.
- Deliverables: original FASTQ, aligned BAM (and index), imputed VCF (and index)