combineOutput: Combine output of different variant calling tools

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

Combine output of different variant calling tools

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)

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