SnpRecode

SnpRecode converts genotype data into Fimpute-compatible formats and computes genotype correlations to assess genotype imputation accuracy.

Key Features:

• Format conversion: Converts genotype data into formats compatible with Fimpute to prepare datasets for imputation.
• Genotype correlation calculation: Computes rapid genotype correlation statistics to estimate imputation accuracy.
• Correlation plotting: Generates plots that visualize genotype correlations and imputation accuracy.
• Implementation: Implemented in Python.

Scientific Applications:

• Genotype imputation preprocessing: Preparing genotype datasets for imputation with Fimpute by converting formats.
• Imputation accuracy assessment: Estimating and visualizing imputation accuracy using genotype correlations and plots.
• Quality control of imputed datasets: Evaluating the reliability of imputed genotypes prior to downstream analyses.

Methodology:

Converts genotype formats for Fimpute, computes genotype correlations, and generates correlation plots; implemented in Python.