calculateMappingBiasGatk4 {PureCN} | R Documentation |
Function calculate mapping bias for each variant in the provided panel of normals GenomicsDB.
calculateMappingBiasGatk4( workspace, reference.genome, min.normals = 1, min.normals.betafit = 7, min.normals.assign.betafit = 3, min.normals.position.specific.fit = 10, min.median.coverage.betafit = 5, num.betafit.clusters = 9, min.betafit.rho = 1e-04, max.betafit.rho = 0.2, AF.info.field = "AF" )
workspace |
Path to the GenomicsDB created by |
reference.genome |
Reference FASTA file. |
min.normals |
Minimum number of normals with heterozygous SNP for calculating position-specific mapping bias. |
min.normals.betafit |
Minimum number of normals with heterozygous SNP fitting a beta distribution |
min.normals.assign.betafit |
Minimum number of normals with heterozygous SNPs to assign to a beta binomal fit cluster |
min.normals.position.specific.fit |
Minimum normals to use position-specific beta-binomial fits. Otherwise only clustered fits are used. |
min.median.coverage.betafit |
Minimum median coverage of normals with heterozygous SNP for fitting a beta distribution |
num.betafit.clusters |
Maximum number of beta binomial fit clusters |
min.betafit.rho |
Minimum dispersion factor rho |
max.betafit.rho |
Maximum dispersion factor rho |
AF.info.field |
Field in the |
A GRanges
object with mapping bias and number of normal
samples with this variant.
Markus Riester
## Not run: resources_file <- system.file("extdata", "gatk4_pon_db.tgz", package = "PureCN") tmp_dir <- tempdir() untar(resources_file, exdir = tmp_dir) workspace <- file.path(tmp_dir, "gatk4_pon_db") bias <- calculateMappingBiasGatk4(workspace, "hg19") saveRDS(bias, "mapping_bias.rds") unlink(tmp_dir, recursive=TRUE) ## End(Not run)