In this article you will find information on the different types of configuration pipelines for the Maize species. The configuration include:
Maize low-pass v1.1
- Same as Maize low-pass v1.0 but with multi-allelic SNPs included in the imputation reference panel.
Maize low-pass v1.0
- Reference genome: AGPv4
- Imputation reference panel: Maize 282 association panel genotypes (7x, AGPv4 coordinates), for a total of ~82M variants.
- Strain reference panel: Each strain in the imputation reference panel was considered a separate population. Those that appear particularly similar are merged downstream into related groups such as "NC262RELATED".
- Deliverables: original FASTQ, aligned BAM (and index), imputed VCF (and index), strain analysis