method_homopolymer_indels: Get indels in homopolymers

In vladimirsouza/lrRNAseqBenchmark: Figure out how to call varaints from Iso-Seq data

Get indels in homopolymers

Description

Create a new data.frame that stores deletions of inside homopolymers, and insertions of a same nucleotide type that happen inside homopolymers of that same nucleotide type. Homopolymer length equal to 1 means non-homopolymers.

Usage

method_homopolymer_indels(
  input_table,
  first_method_name,
  second_method_name,
  vcf_first,
  vcf_second,
  method_dataset_name,
  homopolymers,
  ref_fasta_seqs,
  min_isoseq_coverage,
  genotyped_alt
)

Arguments

input_table	A data.frame. The input master table.
first_method_name	A 1-length string of the name of a method. First, the variant information that is taken is related to this method. If a variant is not called by the method, its information is taken relating to the method specifiec in 'second_method_name'.
second_method_name	A 1-length string. The name of a method.
vcf_first	A 1-length string. The path of the VCF file of the first method.
vcf_second	A 1-length string. The path of the VCF file of the second method.
method_dataset_name	A 1-length string. Name of the dataset used to call variants by the methods to be compared.
homopolymers	A CompressedIRangesList object. It should store all homopolymers, it's nucleotive types and lengths, of the genome used as the reference to call the variants. It is gerated by the function 'sarlacc::homopolymerFinder'.
ref_fasta_seqs	A DNAStringSet object. The sequences of the genome used as the reference to call the variants. It's names must be in the form like "chr1", "chr2", ..., "chrX", "chrY".
min_isoseq_coverage	min iso-seq read coverage to filter.
genotyped_alt	One of the strings "find" or "same". If "find", the function finds the correct alternative allele based on the genotype. This option must be chosen if there are multiple values for column ALT, which is the case of VCF files output by DeepVariant and Clair3. Since GATK's VCF files keep only the genotyped alternative allele in column ALT, this argument should be "same".

Value

A data.frame.

vladimirsouza/lrRNAseqBenchmark documentation built on March 23, 2023, 7:32 a.m.