Package index • lantern

Step 1: split Split a VCF (or raw genotype/ancestry matrices) by local ancestry. ancestry_split() and the K-population split_*_multi() primitives work for any number of populations, not just two.
`ancestry_split()`	Split a phased VCF by local ancestry (Step 1)
`ancestry_split_dosage()`	Run ancestry splitting pipeline
`ancestry_split_phased()`	Run phased ancestry splitting pipeline
`split_diploid()`	Split genotype matrix by ancestry
`split_diploid_multi()`	Split unphased genotype matrix by ancestry for K populations
`split_haplotype()`	Split phased haplotypes by ancestry
`split_haplotype_multi()`	Split phased haplotypes into K population-specific dosage matrices
`read_bed_file()`	Read a PLINK .bed file of BED-encoded local ancestry calls
Step 2: write GDS Materialize a Step 1 split result to per-population GDS files.
`write_ancestry_gds()`	Write all populations of an ancestry split to GDS files (Step 2)
`write_dosage_gds()`	Write an ancestry-specific dosage matrix to a SeqArray GDS file
Step 3: associate Run GMMAT::SMMAT() across ancestry-split GDS files and Cauchy-combine the per-gene p-values.
`ancestry_smmat()`	Run ancestry-stratified SMMAT + Cauchy combination (Step 3)
`cauchy_combine()`	Cauchy combination test for multiple p-values
Package
`lantern` `lantern-package`	lantern: Ancestry-Specific Rare Variant Analysis

Reference