combineOutput: Combine output of different variant calling tools

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

Description

appreci8R combines and filters the output of different variant calling tools according to the 'appreci8'-algorithm. In the 4th analysis step, all normalized and annotated calls of the different variant calling tools are combined. A GRangesObject with all combined calls is returned.

Usage

combineOutput(output_folder, caller_names, annotated_calls_g)

Arguments

output_folder	The folder to write the output files into. If an empty string is provided, no files are written out.
caller_names	Vector containing the name of the variant calling tools.
annotated_calls_g	A GRangesList object. Every list element contains the variant calls of one variant calling tool. Annotate()-output can directly be taken as input. Providing a list with only one list element, i.e. evaluating only one variant calling tool, is possible, but not assumed to be useful. The point of the appreci8-algorithm lies in the combined evaluation and filtration of the output of several variant calling tools.

Details

The function combineOutput performs a combination of the normalized and annotated variant calls from different variant calling tools. The results are sorted according to Chr, Pos, Ref, Alt and SampleID. If two callers - caller1 and caller2 - report the same variant for the same sample, it is only reported once in the output file with a “1” in the column “caller1” and another “1” in the column “caller2”.

Value

A GRanges object is returned containing all combined calls. Reported metadata columns are: SampleID, Ref, Alt, Location, c. (position of variant on cDNA level), p. (position of variant on protein level), AA_ref, AA_alt, Codon_ref, Codon_alt, Consequence, Gene, GeneID, TranscriptID. In addition, one column for every variant calling tool is reported, containing a “1” for every call detected by that tool and “NA” for every call not detected by that tool.

If an output folder is provided, the output is saved as Results_Raw.txt.

Author(s)

Sarah Sandmann <[e-mail]>

See Also

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

Examples

library("GenomicRanges")
gatk<-GRanges(seqnames = c("4","X"),
              ranges = IRanges(start = c(106196951,15838366),
                               end = c(106196951,15838366)),
              SampleID = c("Sample2","Sample1"),
              Ref = c("A","C"),
              Alt = c("G","A"),
              Location = c("coding,coding","coding"),
              c. = c("5284,5347","864"),
              p. = c("1762,1783","288"),
              AA_ref = c("I,I","N"),
              AA_alt = c("V,V","K"),
              Codon_ref = c("ATA,ATA","AAC"),
              Codon_alt = c("GTA,GTA","AAA"),
              Consequence = c("nonsynonymous,nonsynonymous","nonsynonymous"),
              Gene = c("TET2,TET2","ZRSR2"),
              GeneID = c("54790,54790","8233"),
              TranscriptID = c("18308,18309","75467"))
varscan<-gatk[2,]
annotated<-GRangesList()
annotated[[1]]<-gatk
annotated[[2]]<-varscan

combined<-combineOutput("", c("GATK","VarScan"), annotated)

appreci8R documentation built on Nov. 8, 2020, 11:10 p.m.