Chunk #14 — Methods — Efficient Retrieval of Summary Association Statistics and Sequence Variants

Source

SEQMINER: An R-Package to Facilitate the Functional Interpretation of Sequence-Based Associations.

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In this function, vcfColumn allows users to specify descriptive columns in VCF files to be extracted. These columns include CHROM, POS, and ID. The option vcfInfo allows users to choose fields in the INFO field from VCF files. These fields may include (but are not limited to) allele frequencies (AF), annotation information (ANNO), etc. Finally, vcfIndv allows users to specify fields defined in the FORMAT column to be extracted. Examples include genotypes (GT), genotype likelihoods (GL), allelic depth (AD), etc.