lollipopPlot can not show in_frame_del mutation

[Suke-fudan]

Describe the issue

Chr Start End Ref Alt Func.refGene Gene.refGene GeneDetail.refGene ExonicFunc.refGene AAChange.refGene cytoBand
chr19 17753696 17753698 CTC - exonic UNC13A . nonframeshift deletion UNC13A:NM_001080421:exon19:c.2428_2430del:p.E810del 19p13.11
chr19 17774376 17774376 C T exonic UNC13A . nonsynonymous SNV UNC13A:NM_001080421:exon8:c.G524A:p.C175Y 19p13.11

Here is a tab delimited annovar file. I want to show the two mutions using lollipopPlot.

I was confused because I tried many times and each time I could only draw the missense mutation but not the in_frame_del mutation(There is only the missense mutation in the plot). I checked, in the C_var.annovar.maf file, there are two mutations, the difference is that the "Variant_Type" of the in_frame_del mutation is listed as "NA".

Command

C_var.annovar.maf = annovarToMaf(annovar = "2.hg19_multianno_1.txt", 
                                     Center = "NA", refBuild = "hg19", 
                                     table = "refGene", sep = "\t")
write.table(x=C_var.annovar.maf,file="C_var_annovar_maf",
            quote= F,sep="\t",row.names=F)
var_maf = read.maf("C_var_annovar_maf")
p <- lollipopPlot(maf = var_maf, gene = 'UNC13A', AACol = 'aaChange', refSeqID = 'NM_001080421',
                  proteinID = 'NP_001073890',showMutationRate = TRUE)

Session info
Run sessionInfo() and post the output below

R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

ggplot2_3.4.2
maftools_2.14.0

[PoisonAlien]

Hi,
Thanks for the issue and sorry for the delay.
I have updated the annovarToMaf and it should now better handle indels. I hope this helps.