calculateMappingBiasVcf {PureCN} | R Documentation |
Function calculate mapping bias for each variant in the provided panel of normals VCF.
calculateMappingBiasVcf( normal.panel.vcf.file, min.normals = 1, min.normals.betafit = 7, min.median.coverage.betafit = 5, yieldSize = 5000, genome )
normal.panel.vcf.file |
Combined VCF file of a panel of normals, reference and alt counts as AD genotype field. Should be compressed and indexed with bgzip and tabix, respectively. |
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.median.coverage.betafit |
Minimum median coverage of normals with heterozygous SNP for fitting a beta distribution |
yieldSize |
See |
genome |
See |
A GRanges
object with mapping bias and number of normal
samples with this variant.
Markus Riester
normal.panel.vcf <- system.file("extdata", "normalpanel.vcf.gz", package="PureCN") bias <- calculateMappingBiasVcf(normal.panel.vcf, genome = "h19") saveRDS(bias, "mapping_bias.rds")