metrics_alignqc: Generate quality control metrics for aligned sequences

In TearsWillFall/ULPwgs: An implementation of a wrapper for estimating tumor fraction in ultra-low-pass whole genome sequencing (ULP-WGS) for cell-free DNA in GNU/Unix based systems

Generate quality control metrics for aligned sequences

Description

This function generates quality control metrics for an aligned sequence. Works for WGS and Panel data. WGS metrics will be generated if bait and target intervals are nor given, otherwise Panel metrics will be generateds. Target and bait BEDs can be converted to interval format using Picards BedToIntervalList functions. For example java -jar ~/tools/picard/build/libs/picard.jar BedToIntervalList I=PCFv2newchem_primary_targets.bed O=PCFv2newchem_primary_targets.interval_list SD=~/Scratch/RefGenome/hs37d5.fa For more information about interval format check: https://gatk.broadinstitute.org/hc/en-us/articles/360036883931-BedToIntervalList-Picard-

Usage

metrics_alignqc(
  bin_samtools = build_default_tool_binary_list()$bin_samtools,
  bin_picard = build_default_tool_binary_list()$bin_picard,
  bin_bedtools = build_default_tool_binary_list()$bin_bedtools,
  ref_genome = build_default_reference_list()$HG19$reference$genome,
  bam = "",
  output_dir = ".",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  tmp_dir = ".",
  mapq = 0,
  bi = build_default_reference_list()$HG19$panel$PCF_V3$intervals$bi,
  ti = build_default_reference_list()$HG19$panel$PCF_V3$intervals$ti,
  ri = build_default_reference_list()$HG19$rnaseq$intervals$ri,
  ref_flat = build_default_reference_list()$HG19$rnaseq$reference$ref_flat,
  method = "tg",
  mode = "local",
  executor_id = make_unique_id("alignQC"),
  task_name = "alignQC",
  time = "48:0:0",
  threads = 3,
  ram = 4,
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

bin_samtools	Path to samtools executable. Default path tools/samtools/samtools.
bin_picard	Path to picard executable. Default path tools/picard/build/libs/picard.jar.
bin_bedtools	Path to bedtools executable. Default path tools/bedtools2/bin/bedtools. Only required if analyzing panel data.
ref_genome	Path to input file with the reference genome sequence.
bam	Path to the BAM file.
output_dir	Path to the output directory.
verbose	Enables progress messages. Default False.
tmp_dir	Path to tmp directory.
mapq	Minimum MapQ for Picard Wgs metrics. Default 0.
bi	Bait capture target interval for panel data. Requires ti and off_target and on_tar arguments. Interval format.
ti	Primary target intervals for panel data. Requires bi and off_tar and on_tar argmunets. Interval format.
ri	Path to ribosomal intervals file. Only for RNAseq.
ref_flat	Path to flat refrence. Only for RNAseq.
mode	Type of data to generate metrics for. Default tg. Options "wgs","tg","rna"
executor_id	Task EXECUTOR ID. Default "gatherBAM"
task_name	Task name. Default "gatherBAM"
ram	RAM in GB to use. Default 4 Gb.
thread	Threads to use. Default 3.

Details

Off target BED can be created by generating the complementary regions from the target BED using bedtools complement function. For example ~/tools/bedtools2/bin/bedtools complement -i PCFv2newchem_capture_targets.bed -g ~/Scratch/RefGenome/hs37d5.fa.fai > Probes_Off_target_regions.bed Note: This BED has to be sorted using the same reference as the BAM files. Using different reference to generate the BED from the one used to align the BAM may cause issues even when sorted due to scaffold chromosomes.

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