GB/T 12715-1991
Abolished
T/LTIA 22-2023
Active
Group standards
T/LTIA 22-2023 The application technology specifications for low-depth sequencing data of crowd are as follows: whole-genome association analysis
T/LTIA 22-2023 The application technology specifications for low-depth sequencing data of crowd are as follows: whole-genome association analysis
Price:
$ 20.00
Basic Information
Standard Code:
T/LTIA 22-2023
Standard Type:
Group standards
Standard Status:
Active
is_force_gb:
no
CCS Name:
-
ICS Name:
Biology, botany, and zoology
Publish Date:
2023-10-17
Implement Date:
2023-11-17
Scope
Scope: This document provides a technical process for applying ultra-low depth sequencing data from a population to genome-wide association analysis. This document provides technical methods for detecting population variants and inferring genotypes from ultra-low depth sequencing data from a population. This document is applicable to the mining applications of ultra-low depth sequencing data from a population, but not to high-depth sequencing data applications. Main technical content: In the terms and definitions section, definitions are provided for ultra-low depth sequencing data, sequencing error rate, DNA contamination rate, alignment quality value, and variant detection. In the abbreviations section, the English full name and abbreviations of genotype file format, genotype dosage, principal component analysis, genome-wide association analysis, minor allele frequency, and Hardy-Weinberg equilibrium law are provided. In the process of ultra-low depth sequencing data and its application in genome-wide association analysis, the standard describes in the form of a flowchart the entire process from inputting the original FASTQ format file of sequencing data to completing genome-wide association analysis, which mainly involves steps such as sequence alignment and genotype inference. Three key quality control steps are proposed: sample inclusion criteria, BAM quality control, and inclusion requirements for variant sites in genome-wide association analysis. In the section on sample inclusion criteria, specific numerical limits or recommendations are proposed for samples that can be included in the analysis based on indicators such as sequencing depth and DNA contamination rate. In the section on BAM quality control, numerical limits are proposed for sequences in terms of read length and alignment quality value. In the section on inclusion requirements for variant sites in genome-wide association analysis, specific numerical recommendations are proposed based on minor al