SOW.pdf
PDF 155 KB Posted
- Attached to
- Data Analysis and Harmonization Services for the Alzheimer’s Disease Sequencing Project (ADSP)
- Solicitation number
- Not on record
About this file
This is a Statement of Work for data analysis and harmonization services supporting the Alzheimer's Disease Sequencing Project (ADSP), a National Institutes of Health-funded initiative. The contract period runs from August 1, 2026 through July 31, 2027.
The contractor must perform genome analysis and harmonization on 4,799 unaligned raw sequencing data samples from Vanderbilt University Medical Center and the National Alzheimer's Coordinating Center. Services include processing raw sequencing data using Amazon Cloud infrastructure with ADSP SNV/INDEL and SV calling pipelines, including format conversion (CRAM to BAM), read remapping using BWA, duplicate marking, base calling quality score calibration using GATK BQSR, indel realignment using GATK IndelRealigner, SNV and indel calling using GATK HaplotypeCaller, and structural variant calling using Streka, Manta, and Smoove. The contractor must perform quality assurance checks (sex check, contamination check, and relatedness checks) and stage sequencing data on Amazon S3 standard storage for two months. Storage requirements include up to 50GB per genome for total storage space, 30GB for CRAM sequence read alignment, 10GB each for genomic VCF files from GATK and ATLAS genotype callers, with three-year retention on Amazon S3 and Glacier. The processed samples must be directly comparable with the existing ADSP combined dataset to maintain full methodology continuity. The contractor must provide a dedicated project manager as point of contact and submit a summary of results at contract conclusion. Monthly meetings with the National Institute on Aging are required. The government will provide 4,799 FASTQ files of unaligned raw sequence data via electronic cloud transfer.
View the file
Other files
| File | Type | Posted |
|---|---|---|
| NOI.pdf |
On GovTribe
Work with this file
- Download the original file
- Contacts named in this file
- Similar government files
- Ask GovTribe AI about this file
Text version
Version 11-30-2016-1 FAR Part 11—Describing Agency Needs
STATEMENT OF WORK
GENERAL INFORMATION
Title of Project:
Data Analysis and Harmonization Services
Statement of Need and Purpose:
Alzheimer’s Disease Sequencing Project (ADSP) is a large, NIH-funded effort to uncover the genetic architecture of Alzheimer’s disease by sequencing and analyzing DNA from tens of thousands of individuals. Contractor will provide data processing and data storage related to the ADSP project.
Background Information and Objective:
ADSP is a massive multi-cohort genomic dataset built from diverse Alzheimer’s populations designed to uncover genetic drivers of disease continuously expanding in scale, diversity, and datas types. As more samples are added to the dataset, samples need to be harmonized by making data from different studies, cohorts, or platforms consistent, comparable, and usable together. Data analysis and harmonization is essential because ADSP data comes from dozens of cohorts collected over many years using different methods.
Period of Performance:
August 1, 2026 through July 31, 2027
SCOPE OF WORK
General Requirements:
Independently and not as an agent of the Government, the Contractor shall furnish all the necessary services, qualified personnel, material, equipment, and facilities, not otherwise provided by the Government as needed to perform the Statement of Work below.
Specific Requirements:
The Contractor shall perform genome analysis and storage on 4799 unaligned raw sequencing data from Vanderbilt University Medical Center and National Alzheimer’s Coordinating Center.
Contractor’s services must include specifications as follows:
• ADSP genome analysis and harmonization shall be carried out on Amazon Cloud using the ADSP SNV/INDEL and SV calling pipelines
• ADSP genome analysis and harmonization shall process raw sequencing data (Convert CRAM to BAM format, read remapping using BWA, sorting reads, marking duplicates)
• ADSP genome analysis and harmonization shall calibrate base calling quality scores using GATK BQSR and realigning reads around known indels using GATK IndelRealigner.
• ADSP genome analysis and harmonization shall call SNVs and Indels using GATK HaplotypeCaller
• ADSP genome analysis and harmonization shall call SVs using programs such as Streka, Manta and Smoove
• ADSP genome analysis and harmonization shall include quality assurance checks (sex check, contamination check, relatedness checks) on the processing genome
• ADSP genome analysis and harmonization shall include staging of sequencing data on Amazon S3 standard storage for 2 months
• ADSP storage shall include up to 50GB of storage space per genome.
• ADSP storage shall include up to 30GB of CRAM sequence read alignment
• ADSP storage shall include up to 10GB of genomic VCF produced by GATK genotype caller
• ADSP storage shall include up to 10GB of genomic VCF produced by ATLAS genotype caller
• ADSP storage shall include Amazon cloud storage on S3, and Glacier for three years.
• The Government’s 4799 samples shall be directly comparable with all the ADSP combined set of sequencing datasets to maintain full methodology continuity with the existing ADSP dataset.
LEVEL OF EFFORT:
To accomplish these requirements, the Contractor shall provide dedicated project manager to coordinate genome analysis and storage.
GOVERNMENT RESPONSIBILITIES
The government will provide 4799 FASTQ files of unaligned raw sequence data to the Contractor via electronic cloud transfer
DELIVERY OR DELIVERABLES
Genome analysis and harmonization of 4799 samples with all existing ADSP samples and storage on Amazon cloud services
REPORTING REQUIREMENTS
The Contractor will meet with NIA in monthly recurring meetings and over email to discuss results. A summary of the results will be provided at the end of the contract period.
OTHER CONSIDERATIONS
Travel:
The principal place of performance is the vendor’s work site. Travel for contractor employees will not be necessary.
Key Personnel:
Vendor will provide a dedicated project manager to the government as a point of contact for the services.
| SCOPE OF WORK |
| DELIVERY OR DELIVERABLES |
File details come from the government source that posted it. Updated .