pcangsd

Description

pcangsd website

Framework for analyzing low-depth next-generation sequencing (NGS) data in heterogeneous/structured populations using principal component analysis (PCA). Population structure is inferred by estimating individual allele frequencies in an iterative approach using a truncated SVD model. The covariance matrix is estimated using the estimated individual allele frequencies as prior information for the unobserved genotypes in low-depth NGS data.

Environment Modules

Run module spider pcangsd to find out what environment modules are available for this application.

Environment Variables

• HPC_PCANGSD_DIR - installation directory
• HPC_PCANGSD_BIN - executable directory

Categories

biology