Attachment 001 Specifications Cattle Genotypes Imputed From Low Coverage DNA Sequencing.pdf

Attachment 001 Specifications

Cattle Genotypes Imputed from Low-Coverage DNA Sequencing

GENERAL INFORMATION

1.0 Background and Purpose:

Scientists at the Roman L. Hruska U.S. Meat Animal Research Center (USMARC) are developing scientific information and new technology to solve high priority problems for the U.S. beef, sheep, and swine industries. As part of this effort they require genotypes imputed from low-coverage sequence to a comprehensive set of sequence variants detected in a large reference panel assembled from diverse cattle with high-coverage DNA sequence.

CONTRACTOR REQUIREMENTS

2.0 Technical Requirements/Tasks:

The Contractor shall provide 0.4x or more coverage DNA sequence on 1,000 samples, and imputed genotypes and genotype probabilities for at least 50 million DNA sequence variants detected in a reference panel having at least 1500 animals, including representatives of Angus, Hereford, Simmental, Charolais, Limousin, Gelbvieh, Brahman and Brahman-influenced beef breeds. Results will be in the form of

• a complete copy of raw sequence in FASTQ format

• a complete copy of imputed genotypes in VCF format

3.0 Deliverable / Schedule/ Address:

Facility address is listed below:

USMARC

844 Road 313

Clay Center NE 68933

Key Deliverables

Item No.

Deliverable

Objective

Due

1 Imputed genotypes per the technical requirements

Sequence variant genotypes for 1,000 samples per the technical requirements

06/15/2021 –

08/31/2021

4.0 Government Furnished:

1) 1,000 DNA samples.

5.0 Performance Requirement Measures:

Electronic access to formatted low-coverage sequence and genotypes imputed per technical requirements within the expected delivery time.