In this article you will find information on the different types of configuration pipelines for the Feline species. The configurations include:
Version 2
Domestic cat low-pass v2.0
- Reference genome: same as Domestic cat low-pass v1.0
- Imputation reference panel: We used 185 WGS samples from Felis Catus breeds from the 99 lives project (a partial list can be found here) using GATK4 into a reference panel comprising 55M SNPs and small indels.
- Deliverables: original FASTQ, aligned BAM (and index), imputed VCF (and index)
Version 1
Domestic cat low-pass v1.0
- Reference genome: felCat9
- Imputation reference panel: We used 78 WGS samples from Felis Catus breeds from the 99lives project and processed these data using GATK4 into a reference panel of 49M snps and small indels.
- Deliverables: original FASTQ, aligned BAM (and index), imputed VCF (and index)