process_cnvkit: This function functions calls Mutect2 for variant calling. If...

View source: R/cnvkit.R

process_cnvkitR Documentation

This function functions calls Mutect2 for variant calling. If a vector of tumour samples are provided these will be processed in multi-sample mode. To run in tumour-normal mode suppply a single tumour and normal sample. If no normal is supplied this will run in tumour only. TO DO// Implement mitochondrial mode feature

Description

For more information read: https://cnvkit.readthedocs.io/en/stable/pipeline.html

Usage

process_cnvkit(
  target = build_default_reference_list()$HG19$panel$PCF_V3$binned$target,
  antitarget = build_default_reference_list()$HG19$panel$PCF_V3$binned$antitarget,
  ref_genome = build_default_reference_list()$HG19$reference$genome,
  access = build_default_reference_list()$HG19$reference$access_5k,
  sif_cnvkit = build_default_sif_list()$sif_cnvkit,
  pon = build_default_reference_list()$HG19$panel$PCF_V3$variant$pon_cn_male,
  bam = NULL,
  patient_id = NULL,
  seg_method = "cbs",
  seq_method = "hybrid",
  diagram = TRUE,
  scatter = TRUE,
  read_count = FALSE,
  min_mapq = 0,
  gc = TRUE,
  edge = TRUE,
  rmask = TRUE,
  smooth = FALSE,
  drop_low_coverage = TRUE,
  drop_outliers = 10,
  range_scatter = NULL,
  range_list_scatter = NULL,
  genes_scatter = NULL,
  margin_width_scatter = 1e+06,
  plot_by_bin_scatter = FALSE,
  trend_scatter = FALSE,
  antitarget_symbol_scatter = "@",
  segment_colour_scatter = "red",
  y_max_scatter = NULL,
  y_min_scatter = NULL,
  cn_thr_diagram = 0.5,
  min_probes_diagram = 3,
  male_reference_diagram = FALSE,
  gender_diagram = "male",
  shift_diagram = TRUE,
  ...
)

Arguments

ref_genome

REQUIRED Path to reference genome fasta file.

access

OPTIONAL Path to reference genome accessibility. Default none

sif_cnvkit

REQUIRED Path to cnvkit sif file.

pon

OPTIONAL Path to panel of normal.

seg_method

OPTIONAL Method to use to generate segmentation calls.Default cbs. Options "cbs","flasso","haar","none","hmm","hmm-tumor","hmm-germline"

seq_method

OPTIONAL Sequenced methods used. Default hybrid. Options "hybrid","amplicon","wgs"

range_scatter

OPTIONAL Range to show in chr:start-end format. Default none

range_list_scatter

OPTIONAL Path to BED file with range list. Default none

genes_scatter

OPTIONAL List of genes to focus on. Default none.

margin_width_scatter

OPTIONAL Default gene margin width. Default 1000000

plot_by_bin_scatter

OPTIONAL Assume all bins are the same size. Default FALSE

trend_scatter

OPTIONAL Show trendline. Default TRUE.

antitarget_symbol_scatter

OPTIONAL Show antitarget probes with this symbol. Default "@"

segment_colour_scatter

OPTIONAL Show antitarget probes with this symbol. Default "@"

y_max_scatter

OPTIONAL Y max range. Default NULL.

y_min_scatter

OPTIONAL Y min range. Default NULL.

cn_thr_diagram

OPTIONAL Copy number threshold. Default 0.5

min_probes_diagram

OPTIONAL Minimum number of probes to show a gene. Default 3

male_reference_diagram

OPTIONAL Assume inputs were normalized to a male reference. Default FALSE

gender_diagram

OPTIONAL Assume sample gender. Default male

shift_diagram

OPTIONAL Adjust the X and Y chromosomes according to sample sex. Default TRUE

tumour

REQUIRED Path to tumour BAM file.

normal

OPTIONAL Path to normal BAM file.

rdata

OPTIONAL Import R data information with list of BAM.

selected

OPTIONAL Select BAM from list.

output_name

OPTIONAL Name for the output. If not given the name of the first tumour sample of the samples will be used.

output_dir

OPTIONAL Path to the output directory.

normal_ichor

OPTIONAL Path to normal samples. Default c(0.5,0.6,0.7,0.8,0.9)

ploidy_ichor

OPTIONAL Initial tumour ploidy; can be more than one value if additional ploidy initializations are desired. Default: 2

lambda_ichor

OPTIONAL Initial Student's t precision; must contain 4 values (e.g. c(1500,1500,1500,1500)); if not provided then will automatically use based on variance of data

scStates_ichor

OPTIONAL Subclonal states to consider. Default NULL

output_name_ichor

OPTIONAL Name for the output. If not given the name of the first tumour sample of the samples will be used.

lambdaScaleHyperParam_ichor

OPTIONAL Hyperparameter (scale) for Gamma prior on Student's-t precision. Default 3

maxCN_ichor

OPTIONAL Total clonal states. Default 7.

estimateNormal_ichor

OPTIONAL Estimate normal. Default TRUE.

estimateScPrevalence_ichor

OPTIONAL Estimate subclonal prevalence. Default TRUE.

estimatePloidy_ichor

OPTIONAL Estimate tumour ploidy. Default TRUE.

maxFracGenomeSubclone_ichor

OPTIONAL Exclude solutions with subclonal genome fraction greater than this value. Default 0.5

maxFracCNASubclone_ichor

OPTIONAL Exclude solutions with fraction of subclonal events greater than this value. Default 0.7

minSegmentBins_ichor

OPTIONAL Minimum number of bins for largest segment threshold required to estimate tumor fraction; if below this threshold, then will be assigned zero tumor fraction

altFracThreshold_ichor

OPTIONAL Minimum proportion of bins altered required to estimate tumor fraction; if below this threshold, then will be assigned zero tumor fraction. Default: 0.05

includeHOMD_ichor

OPTIONAL If FALSE, then exclude HOMD state. Useful when using large bins (e.g. 1Mb). Default FALSE.

txnE_ichor

OPTIONAL Self-transition probability. Increase to decrease number of segments. Default: 0.9999999

txnStrength_ichor

OPTIONAL Transition pseudo-counts. Exponent should be the same as the number of decimal places of –txnE. Default: 1e+07

plotFileType_ichor

OPTIONAL File format for output plots. Default pdf

plotYLim_ichor

OPTIONAL ylim to use for chromosome plots. Default: c(-2,2)

threads

OPTIONAL Number of threads to split the work. Default 4

ram

OPTIONAL RAM memory to asing to each thread. Default 4

verbose

OPTIONAL Enables progress messages. Default False.

mode

REQUIRED Where to parallelize. Default local. Options "local","batch"

executor_id

Task EXECUTOR ID. Default "recalCovariates"

task_name

Task name. Default "recalCovariates"

time

OPTIONAL If batch mode. Max run time per job. Default "48:0:0"

update_time

OPTIONAL If batch mode. Job update time in seconds. Default 60.

wait

OPTIONAL If batch mode wait for batch to finish. Default FALSE

hold

OPTIONAL HOld job until job is finished. Job ID.


TearsWillFall/ULPwgs documentation built on April 18, 2024, 3:45 p.m.