VCFArray

VCFArray is a Bioconductor package that represents VCF files as objects derived from the DelayedArray package and DelayedArray class. It converts data entries from VCF file into a DelayedArray-derived data structure. The backend VCF file could either be saved on-disk locally or remote as online resources. Data entries that could be extracted include the fixed data fields (REF, ALT, QUAL, FILTER), information field (e.g., AA, AF…), and the individual format field (e.g., GT, DP…). The array data generated from fixed/information fields are one-dimensional VCFArray, with the dimension being the length of the variants. The array data generated from individual “FORMAT” field are always returned with the first dimension being “variants” and the second dimension being “samples”. This feature is consistent with the assay data saved in SummarizedExperiment, and makes the VCFArray package interoperable with other established Bioconductor data infrastructure.