filterTarget: Excludes all off-target calls from further analysis.

In sandmanns/appreci8R: appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV

Excludes all off-target calls from further analysis.

Description

appreci8R combines and filters the output of different variant calling tools according to the 'appreci8'-algorithm. In the 1st analysis step, all off-target calls are excluded from further analysis. A list of data.frames (one list per sample) with all on-target calls is returned.

Usage

filterTarget (output_folder, caller_name, caller_folder, caller_file_names_add,
              caller_file_type, caller_snv_indel, caller_snv_names_add,
              caller_indel_names_add, caller_chr = 1, caller_pos = 2,
              caller_ref = 4, caller_alt = 5, targetRegions)

Arguments

output_folder	The folder to write the output files into. If an empty string is provided, no files are written out.
caller_name	Name of the variant calling tool (only necessary if an output folder is provided).
caller_folder	Folder containing the variant calling results.
caller_file_names_add	Suffix for naming the variant calling files. If an empty string is provided, it is assumed that the files only contain the sample name, e.g. "Sample1.vcf".
caller_file_type	File type of the variant calling results (".vcf" or ".txt").
caller_snv_indel	SNVs and indels are reported in the same file (TRUE or FALSE).
caller_snv_names_add	Suffix for naming the variant calling files containing SNVs (only evaluated if caller_snv_indel==FALSE).
caller_indel_names_add	Suffix for naming the variant calling files containing indels (only evaluated if caller_snv_indel==FALSE).
caller_chr	Column of the variant calling input containing information on chr (default: 1).
caller_pos	Column of the variant calling input containing information on pos (default: 2).
caller_ref	Column of the variant calling input containing information on ref (default: 4).
caller_alt	Column of the variant calling input containing information on alt (default: 5).
targetRegions	Data.frame object containing the target regions to be analyzed (bed-format: 1st column chr, 2nd column 0-based start pos, 3rd column 1-based end pos). Or: GRanges object containing the target regions to be analyzed.

Details

The function filterTarget covers two steps: reading input and target filtration.

First, all files in caller_folder of the file type caller_file_type with the suffix caller_file_names_add are read. Sample names are automatically derived from the file names (e.g. a sample name would be called "Sample1" if a file was called "Sample1.txt" and no suffix was defined; a sample would be called "Sample1.mutations" if a file was called "Sample1.mutations.vcf" and no suffix was defined, but "Sample1" if the suffix ".mutations" was defined).

If SNVs and indels are reported in separated files (in the same folder), caller_snv_indel==TRUE and caller_snv_names_add and caller_indel_names_add are defined, input from two files per sample is read and automatically combined (e.g. a sample would be called "Sample1" if files "Sample1.SNV.vcf" and "Sample1.indel.vcf" are read and caller_snv_indel==TRUE, caller_snv_names_add was defined as ".SNV" and caller_indel_names_add was defined as ".indel").

Subsequently, the read variant calling results are filtered according to the defined target region. All off-target calls are excluded from further analysis.

Value

A list of data.frames is returned. Every list element contains the information on one sample. Every data.frame contains the columns: the SampleID (taken from the input file names), Chr, Pos, Ref and Alt.

Author(s)

Sarah Sandmann <[e-mail]>

See Also

appreci8R, appreci8Rshiny, normalize, annotate, combineOutput, evaluateCovAndBQ, determineCharacteristics, finalFiltration

Examples

output_folder<-""
target<-data.frame(chr = c("2","4","12","17","21","X"),
                   start = c(25469500,106196950,12046280,7579470,36164400,15838363),
                   end = c(25469510,106196960,12046350,7579475,36164410,15838366))
caller_folder <- system.file("extdata", package = "appreci8R")

targetFiltered<-filterTarget(output_folder, "GATK", caller_folder,
                             ".rawMutations", ".vcf", TRUE, "", "",
                             targetRegions = target)

sandmanns/appreci8R documentation built on Dec. 18, 2024, 3:23 p.m.