In this article you will find information on the different types of configuration pipelines for the Tomato species. The configuration include:
Tomato low-pass SL4.0 v1.0
- Reference genome: SL4.0
- Imputation reference panel: We used 448 WGS samples from the public domain (in particular these studies) and processed these data using GATK4 into a reference panel of 24.4M snps and small indels.
- Deliverables: original FASTQ, aligned BAM (and index), imputed VCF (and index)