callsnvs: Call somatic SNVs by using both global and local error models

In cibiobcg/abemus: Adaptive Base Error Model in Ultra-Deep Sequencing Data

Call somatic SNVs by using both global and local error models

Description

Call somatic SNVs by using both global and local error models

Usage

callsnvs(sample.info.file, outdir, targetbed,
  pbem_dir = file.path(outdir, "BaseErrorModel"),
  controls_dir = file.path(outdir, "Controls"), pacbamfolder_bychrom,
  detection.specificity = 0.995, replicas = 1000,
  replicas.in.parallel = 1, coeffvar.threshold = 0.01,
  AFbycov = TRUE, mincov = 10, mincovgerm = 10, minalt = 1,
  maxafgerm = 0.2, coverage_binning = 50,
  outdir.calls.name = "Results", chrom.in.parallel = 1)

Arguments

sample.info.file	The sample info file listing CASE and CONTROL samples. The format is simply 5 columns, tab-delimited, and there is no column header.
outdir	The folder where outputs will be saved.
targetbed	Genomic regions in the BED tab-delimited format.
pbem_dir	The folder with outputs generated by the compute_pbem function. default: file.path(outdir, "BaseErrorModel")
controls_dir	The folder with outputs generated by the compute_afthreshold function. default: file.path(outdir, "Controls")
pacbamfolder_bychrom	The folder popluted by outputs by the split_pacbam_bychrom function.
detection.specificity	The quantile of the GSE distribution(s) to use to compute the AF threhold. default: 0.995
replicas	Replics sampling to define stability of AF threhold in bins of coverage. default: 1000
replicas.in.parallel	default: 1
coeffvar.threshold	Consider a bin as stable if the coefficient of variations after replicas is lower than the coeffvar.threshold. default: 0.01
AFbycov	Apply coverage-based AF threhold. default: TRUE
mincov	Minimum locus coverage in CASE sample. default: 10
mincovgerm	Minimum locus coverage in CONTROL sample. default: 10
minalt	Minimum number of reads supporting the alternative allele in CASE sample. default: 1
maxafgerm	Maximum allelic fraction observed in matched CONTROL locus. default: 0.2
coverage_binning	Bins of coverage into which divide AFs. default: 50
outdir.calls.name	The subfolder name that will be created in the outdir. default: "Results"
chrom.in.parallel	Number of chromosomes to run in parallel. default: 1

Value

The callsnvs will create a subfolder for each CASE sample within the outdir.calls.name folder. There tab-delimeted files reporting SNV calls passing 3 consecutive filtering steps (pmtab_F1, pmtab_F2 and pmtab_F3) are saved.

The function also return the data.frame tabsnvs_index reeporting for each sample the path to each of the tables generated during the 3 filtering steps.

Examples

sample.info.file <- system.file("extdata", "test_sif_toy.tsv", package = "abemus")
outdir <- tempdir()
targetbed <- system.file("extdata", "regions_toy.bed", package = "abemus")
pacbamfolder_bychrom <- system.file("extdata", "pacbam_data_bychrom", package = "abemus")
pbem_dir <- system.file("extdata", "BaseErrorModel", package = "abemus")
controls_dir <- system.file("extdata", "Controls", package = "abemus")
callsnvs(sample.info.file,outdir,targetbed,pbem_dir,controls_dir,pacbamfolder_bychrom,replicas=1)

cibiobcg/abemus documentation built on Oct. 29, 2022, 9:03 p.m.