PSReliP

PSReliP performs population structure and relatedness analysis from genome-wide genetic variant data to support interpretation in genome-wide association studies (GWAS) and genomic selection.

Key Features:

• Integrated workflow: Integrates analytical steps into a single workflow from data processing to result visualization.
• Data filtering and analysis: Employs PLINK alongside custom shell scripts and Perl programs to process and analyze single nucleotide polymorphisms (SNPs) and small insertions or deletions.
• Visualization capabilities: Provides dynamic visualization via Shiny (R), including interactive tables, plots, and charts for exploration of population structure and relatedness.

Scientific Applications:

• Genome-Wide Association Studies (GWAS): By estimating population stratification and cryptic relatedness, it aids selection of statistical methods to mitigate false positives in GWAS.
• Genomic Selection: In animal and plant breeding programs, it quantifies genetic relationships to improve prediction accuracy for selection.

Methodology:

PSReliP executes an ordered sequence of PLINK commands supported by custom shell scripts and Perl programs for data processing and analysis, with Shiny (R) used for interactive result visualization.