call_ASEQ: Wrapper around ASEQ tool for pileup data.

In TearsWillFall/variantCall: An implementation of a wrapper for variant calling using MuTECT2 and Platypus GNU/Unix based systems

Description

This function takes a VCF and BAM files and generates a pileup for all the variants in the vcf file. See https://demichelislab.unitn.it/lib/exe/fetch.php?media=manual.pdf for ASEQ manual. Two modes: -PILEUP: Default use. Generates a pileup from the BAM file -GENOTYPE: Generates genotype at VCF marked positions The output is a ASEQ pileup format that can be used for downstream analysis. In addition, genotype mode generates a VCF file with all heterozygous calls.

Usage

call_ASEQ(
  vcf = "",
  bin_path = "tools/ASEQ/binaries/linux64/ASEQ",
  bam = "",
  mrq = "",
  mbq = "",
  mdc = "",
  htperc = "",
  pht = "",
  mode = "",
  output_dir = "",
  threads = 3,
  verbose = FALSE
)

Arguments

vcf	REQUIRED Path to vcf file.
bin_path	REQUIRED Path to ASEQ binary. Default tools/ASEQ/binaries/linux64/ASEQ
bam	REQUIRED Path to bam file.
mrq	OPTIONAL Filter by read mapping quality >=. Default value 1. See ASEQ doc.
mbq	OPTIONAL Filter by base quality >=. Default value 1. See ASEQ doc.
mdc	OPTIONAL Filter by coverage per base >=. Default value 1. See ASEQ doc.
htperc	OPTIONAL Heterozigosity test based on percentage. Default value 0.2. Only in GENOTYPE mode. See ASEQ doc.
pht	OPTIONAL P-value for heterozigosity test. Default value 0.2. Only in GENOTYPE mode. See ASEQ doc.
mode	OPTIONAL Usage mode. Default value PILEUP. See ASEQ doc.7
output_dir	OPTIONAL Path to the output directory.
threads	OPTIONAL Number of threads to use. Default value 3.
verbose	OPTIONAL Enables progress messages. Default False.

TearsWillFall/variantCall documentation built on Oct. 15, 2021, 8:51 p.m.