In this article you will find information on the different types of configuration pipelines for the Soy species. The configuration include:
Wm82.a4 Version 1
Soy low-pass Wm82.a4 v1.0
- Reference genome: Wm82.a4.v1
- Imputation reference panel: We used 478 samples from the USDA-GRIN germplasm collection, and processed these data using GATK4 into a reference panel of 25M SNPs and short indels.
- Deliverables: original FASTQ, aligned BAM (and index), imputed VCF (and index)
Wm82.a2 Version 2
Soy low-pass Wm82.a2 v2.0
- Same reference genome as v1.0
- Imputation reference panel: We used 478 samples from the USDA-GRIN germplasm collection, and processed these data using GATK4 into a reference panel of 32M SNPs and short indels.
- Deliverables: original FASTQ, aligned BAM (and index), imputed VCF (and index)
Wm82.a2 Version 1
Soy low-pass Wm82.a2 v1.0
- Reference genome: Wm82.a2.v1
- Imputation reference panel: GmHapMap contains ~11M bi-allelic SNPs identified in around 1000 sequenced accessions.
- Deliverables: original FASTQ, aligned BAM (and index), imputed VCF (and index)