In this article you will find information on the different types of configuration pipelines for the Cattle species. The configuration include:
Version 3
Cattle low-pass v3.0
- Reference genome: ARS-UCD1.2
- Imputation reference panel: We used sequence data from 1,987 animals with publicly-available data, and processed these data using GATK into an imputation reference panel. We then subet this reference panel to the set of variants either 1) segregating in annotated Bos taurus samples or 2) present on public genotyping array manifests. This resulted in a reference panel of 59M variants (SNPs and small indels).
- Breed analysis reference panel: We report ancestry proportions from 13 breeds: Angus, Brahman, Charolais, Gelbvieh, Hereford, Holstein, Jersey, Limousin, Red Angus, Simmental, Braunvieh, Santa Gertrudis, and Shorthorn.
- Deliverables: original FASTQ, aligned BAM (and index), imputed VCF (and index), breed analysis
Version 2
Cattle low-pass v2.4
- Same configuration as Cattle low-pass v2.3, but the reference panel has been updated to include additional polymorphisms in the imputed VCF
Cattle low-pass v2.3
- Same configuration as Cattle low-pass v2.2, but with performance improvements
Cattle low-pass v2.2
- Same configuration as Cattle low-pass v2.0, but includes the Y chromosome
Cattle low-pass v2.0
- Reference genome: ARS-UCD1.2
- Imputation reference panel: We used sequence data from 946 samples from B. taurus and B. indicus-related breeds and processed these data using GATK4 into a reference panel of 59M bi-allelic SNPs.
- Breed analysis reference panel: We report ancestry proportions from 12 breeds: Angus (including red and black Angus), Brahman, Charolais, Gelbvieh, Hereford, Holstein, Jersey, Limousin, Maine Anjou, Simmental, Braunvieh, and Shorthorn.
- Deliverables: original FASTQ, aligned BAM (and index), imputed VCF (and index), breed analysis
Version 1
Cattle low-pass v1.0
- Reference genome: ARS-UCD1.2
- Imputation reference panel: We used sequence data from 484 samples primarily from B. taurus breeds and processed these data using GATK4 into a reference panel of 49M bi-allelic SNPs.
- Breed analysis reference panel: We report ancestry proportions from 13 breeds: Angus, Brahman, Charolais, Gelbvieh, Hereford, Holstein, Jersey, Limousin, Red Angus, Simmental, Braunvieh, Santa Gertrudis, and Shorthorn.
- Deliverables: original FASTQ, aligned BAM (and index), imputed VCF (and index), breed analysis