vcfsim: flexible simulation of all-sites VCFs with missing data.

Abstract excerpt

BACKGROUND: VCFs are the most widely used data format for encoding genetic variation. By design, standard VCFs do not include data from sites where all individuals are homozygous for the reference allele (“invariant sites”) and thus do not differentiate these from sites where data are completely missing. However, missing data are a key feature of biological datasets across all domains of genomics, and many recent...

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