This function performs ancestry analysis of a set of samples ad reports the results.
ethseq.Analysis(
target.vcf = NA,
target.gds = NA,
bam.list = NA,
out.dir = tempdir(),
model.gds = NA,
model.available = NA,
model.assembly = "hg38",
model.pop = "All",
model.folder = tempdir(),
run.genotype = FALSE,
aseq.path = tempdir(),
mbq = 20,
mrq = 20,
mdc = 10,
cores = 1,
verbose = TRUE,
composite.model.call.rate = 1,
refinement.analysis = NA,
space = "2D",
bam.chr.encoding = FALSE
)Logical value indicating the success of the analysis
Path to the sample's genotypes in VCF format
Path to the sample's genotypes in GDS format
Path to a file containing a list of BAM files paths
Path to the folder where the output of the analysis is saved
Path to a GDS file specifying the reference model
String specifying the pre-computed reference model to use
String value indicating the assembly version to download for the pre-build models
String value indicating the population to download for the pre-build models
Path to the folder where reference models are already present or downloaded when needed
Logical values indicating whether the ASEQ genotype should be run
Path to the folder where ASEQ binary is available or is downloaded when needed
Minmum base quality used in the pileup by ASEQ
Minimum read quality used in the piluep by ASEQ
Minimum read count acceptable for genotype inference by ASEQ
Number of parallel cores used for the analysis
Print detailed information
SNP call rate used to run Principal Component Analysis (PCA)
Matrix specifying a tree of ancestry sets
Dimensions of PCA space used to infer ancestry (2D or 3D)
Logical value indicating whether input BAM files have chromosomes encoded with "chr" prefix