summary output dropping genes with only indels

[ctokheim]

It appears the summary output is not saving genes that only have indel mutations.

Gene   	Tumor_Sample   	Tumor_Type     	Chromosome     	Start_Position 	End_Position   	Variant_Classification 	Reference_Allele       	Tumor_Allele   	Protein_Change 	DNA_Change
A1CF   	ICGC_0063      	Pancreatic Adenocarcinoma      	10     	52573738       	52573738       	Missense_Mutation      	C      	T      	p.R401Q	c.?
ABCB4  	TCGA-IB-7897   	Pancreatic Adenocarcinoma      	7      	87074281       	87074282       	Frame_Shift_Indel      	-      	T      	p.S339fs       	c.?