markerdata

Markerdata is a dataset comprising information on genetic markers collected across individuals or samples. Markers can be single nucleotide polymorphisms (SNPs), microsatellites, insertions/deletions, or larger structural variants. Each marker is identified by an identifier, mapped to a genomic position, and characterized by reference and alternate alleles. A markerdata matrix records genotypes or genotype probabilities for each marker in each sample, along with metadata such as allele frequencies and quality metrics.

Common formats include VCF (variant call format), PLINK binary files (.bed/.bim/.fam), and PED/MAP, as well as specialized formats such as BGEN and various CSV/TSV exports. Markerdata may be stored in flat files, hierarchical data formats like HDF5, or within relational databases. Interoperability is aided by reference genomes and standardized annotation for markers.

Quality control and preprocessing typically involve filtering markers by call rate and minor allele frequency, testing for Hardy–Weinberg equilibrium, resolving strand orientation, and removing problematic samples. Imputation and phasing are common steps to infer missing genotypes and resolve haplotypes.

Markerdata underpin many genetic analyses, including genome-wide association studies, linkage and QTL mapping, population structure and ancestry inferences, genotype imputation, and genomic selection in breeding programs.

Because markerdata can identify individuals or families, access is often restricted and subject to consent and privacy protections. Reproducible analyses rely on clear provenance, versioned data, and documented processing pipelines.