INDELS not annotated in annovartomaf

[wangpenhok]

hello , i would like to thank all the contributors who developed this wonderful tool sincerely!
However, when i tried to convert an annovar file, some problem occurred and i would like to share my solutions:

1. INDELs were not correctly annotated in terms of Variant_Type
   I found that none of INDEL.annovar files was correctly annotated, instead the Variant_Type column of genuine INDELS is full of NAs. So i checked the source code:

#original source code:

ann[, Variant_Type := ifelse(
ref_alt_diff == 0 , yes = ifelse(test = Ref != "-" & Alt != "-", yes = "SNP",
no = ifelse(ref_alt_diff < 0 , yes = "INS", no = "DEL")), no = NA)]

it is clearly that the above codes didn't includes all conditions, which only considered what to assign when "ref_alt_diff == 0 " . In this case, so long as "ref_alt_diff" doesn't equal 0 the variant is defined as an NA. This is not exactly how it should be. So I tried to make some amendments, and it turned out working well. Here it is :

ann[, Variant_Type := ifelse(
ref_alt_diff == 0 ,
yes = ifelse(test = Ref != "-" & Alt != "-", yes = "SNP",
no = ifelse(ref== "-" , yes = "INS", no = "DEL")),
no =ifelse(ref_alt_diff < 0, yes = "INS", no = "DEL") )
]

i wish it might help those met up with the same problem, and also hope this problem could be fixed soon!

2. VAF column were defined as "character"
   In the source code, colClasses is defined as ”character“ for all columns in annovar by default, including VAF column which is supposed to be "numeric". And this leads to an error when I tried to plot VAF in oncoplot() function. In this customized process, the mean value of VAFs across samples was calculated, consequently VAF column of "character" class doesn't seem to work well. I changed the default colClasses into NULL, which seemed to pave the way for following analysis. This is definitely not flexible enough, so I hope you can develop a better version to solve this problem!

Thanks again !!! And in any case of confusion, as a non-native speaker I confess that my English is poor and please feel free to ask me ~