stack1kg {ldblock} | R Documentation |
couple together a group of VCFs
stack1kg(chrs = as.character(1:22), index = FALSE, useEBI = TRUE)
chrs |
a vector of chromosome names for extraction from 1000 genomes VCF collection |
index |
logical telling whether VcfStack should attempt to create the local index; for 1000 genomes, the tbi are in the cloud and will be used by readVcf so FALSE is appropriate |
useEBI |
logical(1) defaults to TRUE ... use tabix-indexed vcf from EBI |
VcfStack instance
The seqinfo component of returned stack will have NA for genome. Please set it manually; for useEBI=TRUE this would be GRCh38.
if (interactive()) { st1 = stack1kg() st1 }