#version 2.4
#liftOverProgram=CrossMap(https://sourceforge.net/projects/crossmap/)
#liftOverFile=../data/UCSC_chain/hg19ToHg38.over.chain.gz
#new_reference_genome=../../../database/ucsc_hg38.fa
#liftOverTime=July19,2019
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_Position	End_Position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	t_depth	t_ref_count	t_alt_count	n_depth	n_ref_count	n_alt_count
MTOR	0	.	GRCh38	1	11230122	11230122	+	Intron	DEL	A	A	-			TUMOR	NORMAL	A	A																20	10	10	35	30	5
Unknown	0	.	GRCh38	1	15231481	15231482	+	IGR	DNP	TG	TG	CA			TUMOR	NORMAL	TG	TG																16	11	5	22	21	1
CHD1L	0	.	GRCh38	1	147256563	147256563	+	Splice_Site	SNP	G	G	A			TUMOR	NORMAL	G	G																40	19	21	42	42	0
INHA	0	.	GRCh38	2	219574978	219574979	+	Frame_Shift_Ins	INS	-	-	CT			TUMOR	NORMAL	-	-																93	21	72	51	51	0
BAP1	0	.	GRCh38	3	52403411	52403432	+	Splice_Site	DEL	CCCACCTGTCAGCGCCAGGGGA	CCCACCTGTCAGCGCCAGGGGA	-			TUMOR	NORMAL	CCCACCTGTCAGCGCCAGGGGA	CCCACCTGTCAGCGCCAGGGGA																20	10	10	11	11	0
BAP1	0	.	GRCh38	3	52403686	52403692	+	Frame_Shift_Del	DEL	TGGGTGA	TGGGTGA	-			TUMOR	NORMAL	TGGGTGA	TGGGTGA																20	10	10	11	11	0
BAP1	0	.	GRCh38	3	52409773	52409834	+	Splice_Region	DEL	TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC	TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC	-			TUMOR	NORMAL	TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC	TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC																20	10	10	11	11	0
PIK3CA	0	.	GRCh38	3	179210431	179210432	+	In_Frame_Ins	INS	-	-	ATA			TUMOR	NORMAL	-	-																43	21	22	11	11	0
PIK3CA	0	.	GRCh38	3	179218303	179218303	+	Missense_Mutation	SNP	G	-	A			TUMOR	NORMAL	G	G																43	21	22	11	11	0
TERT	0	.	GRCh38	5	1295113	1295113	+	5'Flank	SNP	G	G	A			TUMOR	NORMAL	G	G																20	10	10	11	11	0
TERT	0	.	GRCh38	5	1295135	1295135	+	5'Flank	SNP	G	G	A			TUMOR	NORMAL	G	G																20	10	10	11	11	0
MAP3K1	0	.	GRCh38	5	56882022	56882024	+	In_Frame_Del	DEL	CAA	CAA	-	rs5868032		TUMOR	NORMAL	CAA	CAA																50	34	16	46	46	0
APC	0	.	GRCh38	5	112839061	112839064	+	Frame_Shift_Del	DEL	AAGA	AAGA	GA			TUMOR	NORMAL	AAGA	AAGA																20	12	8	32	30	2
APC	0	.	GRCh38	5	112839061	112839064	+	Frame_Shift_Del	DEL	AAGA	-	CA			TUMOR	NORMAL	-	-																20	0	8	32	0	2
APC	0	.	GRCh38	5	112839061	112839064	+	Frame_Shift_Del	DEL	AAGA	AAGA	-			TUMOR	NORMAL	AAGA	GA																20	12	8	32	30	0
APC	0	.	GRCh38	5	112839061	112839064	+	Frame_Shift_Del	DEL	AAGA	AAGA	GA			TUMOR	NORMAL	AAGA	-																20	12	8	32	30	0
CCND3	0	.	GRCh38	6	41936044	41936045	+	Missense_Mutation	DNP	AG	AG	CA			TUMOR	NORMAL	AG	AG																50	28	22	48	48	0
MET	0	.	GRCh38	7	116771989	116771989	+	Missense_Mutation	SNP	G	G	C			TUMOR	NORMAL	G	G																47	25	22	99	98	1
FLT3	0	.	GRCh38	13	28034105	28034106	+	In_Frame_Ins	INS	-	-	ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG			TUMOR	NORMAL	-	-																20	10	10	11	11	0
TP53	0	.	GRCh38	17	7675994	7675994	+	Splice_Region	SNP	C	C	A			TUMOR	NORMAL	C	C																42	20	22	19	18	1
