DNP variants result in a mutation position of 0

[malachig]

We may still be getting unexpected mutation position specifically for DNPs.

For example, using version 5.1.0, I see this output for a dinucleotide variant:

Chromosome	Start	Stop	Reference	Variant	Transcript	Transcript Support Level	Transcript Length	Biotype	Ensembl Gene ID	Variant Type	Mutation	Protein Position	Gene Name	HGVSc	HGVSp	HLA Allele	Peptide Length	Sub-peptide Position	Mutation Position	MT Epitope Seq	WT Epitope Seq	Best MT IC50 Score Method	Best MT IC50 Score	Corresponding WT IC50 Score	Corresponding Fold Change	Best MT Percentile Method	Best MT Percentile	Corresponding WT Percentile	Tumor DNA Depth	Tumor DNA VAF	Tumor RNA Depth	Tumor RNA VAF	Normal Depth	Normal VAF	Gene Expression	Transcript Expression	Median MT IC50 Score	Median WT IC50 Score	Median Fold Change	Median MT Percentile	Median WT Percentile	BigMHC_EL WT Score	BigMHC_EL MT Score	BigMHC_IM WT Score	BigMHC_IM MT Score	MHCflurryEL Processing WT Score	MHCflurryEL Processing MT Score	MHCflurryEL Presentation WT Score	MHCflurryEL Presentation MT Score	MHCflurryEL Presentation WT Percentile	MHCflurryEL Presentation MT Percentile	MHCflurry WT IC50 Score	MHCflurry MT IC50 Score	MHCflurry WT Percentile	MHCflurry MT Percentile	MHCnuggetsI WT IC50 Score	MHCnuggetsI MT IC50 Score	MHCnuggetsI WT Percentile	MHCnuggetsI MT Percentile	NetMHC WT IC50 Score	NetMHC MT IC50 Score	NetMHC WT Percentile	NetMHC MT Percentile	NetMHCcons WT IC50 Score	NetMHCcons MT IC50 Score	NetMHCcons WT Percentile	NetMHCcons MT Percentile	NetMHCpan WT IC50 Score	NetMHCpan MT IC50 Score	NetMHCpan WT Percentile	NetMHCpan MT Percentile	NetMHCpanEL WT Score	NetMHCpanEL MT Score	NetMHCpanEL WT Percentile	NetMHCpanEL MT Percentile	PickPocket WT IC50 Score	PickPocket MT IC50 Score	PickPocket WT Percentile	PickPocket MT Percentile	Index	DeepImmuno WT Score	DeepImmuno MT Score	SMM WT IC50 Score	SMM MT IC50 Score	SMM WT Percentile	SMM MT Percentile	SMMPMBEC WT IC50 Score	SMMPMBEC MT IC50 Score	SMMPMBEC WT Percentile	SMMPMBEC MT Percentile	Problematic Positions	cterm_7mer_gravy_score	max_7mer_gravy_score	difficult_n_terminal_residue	c_terminal_cysteine	c_terminal_proline	cysteine_count	n_terminal_asparagine	asparagine_proline_bond_count
chr3	147391174	147391176	GC	AA	ENST00000383075.8	1	334	protein_coding	ENSG00000174963	missense	KH/NY	253-254	ZIC4	ENST00000383075.8:c.759_760delinsTT	ENSP00000372553.3:p.Lys253_His254delinsAsnTyr	HLA-A*30:01	8	9	0	YSHVHTSD	HSHVHTSD	NetMHCcons	10641.85	2607.06	0.245	PickPocket	19.0	15.0	1563	0.02	NA	NA	405	0.004	0.038	0.0	20694.92	13233.27	0.639	45.475	26.625	0.00012698365	0.0001307598	0.024284748	0.0387821	0.0075560808181762	0.0344556234776973	0.0032115149949986	0.0035674401939518	99.28660326086955	99.28660326086955	32401.783237890908	32060.39414712895	56.20562500000002	51.47550000000002	16446.35	28991.84	22.25	47.95	9949.02	21366.31	10.0	30.0	2607.06	10641.85	9.2	29.0	14987.38	20023.53	31.0	43.0	0.000178	0.000111	50.0	57.0	11479.159325780087	13648.772779138171	15.0	19.0	57.ZIC4.ENST00000383075.8.missense.253-254KH/NY	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	None	-1.1428571428571428	-0.8285714285714286	False	False	False	0	False	0

Column 20, Mutation Position == 0