[Vcftools-help] convert pacbio VCF3.3 to VCF 4.x

[Stephane P. | V. | <ste...@vi...>]

Dear list,
PacBio gffToVcf produces a weird VCF 3.3 format with additional letters (ID..) to describe the change in the ALT field as well as unexpected dots.
Is there a tool to convert this format to common VCF syntax without loss? when I use the data to xompare it to public data, the letters and dots lead to errors
Thanks

Stephane

example 3.3 content:
##fileformat=VCFv3.3
##fileDate=2017121
##source=gffToVcf --resolved-tool-contract /opt/pacbio/userdata/jobs_root/000/000096/tasks/genomic_consensus.tasks.gff2vcf-0/resolved-tool-contract.json
##INFO=NS,1,Integer,"Number of Samples with Data"
##INFO=DP,1,Integer,"Total Depth of Coverage"
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
chromosome_2	486515	.	C	T	93.00	0	NS=1;DP=47
chromosome_2	487451	.	C	D1	93.00	0	NS=1;DP=47
chromosome_2	511331	.	.	IA	41.00	0	NS=1;DP=52
chromosome_2	537571	.	.	IA	55.00	0	NS=1;DP=40
chromosome_2	636693	.	A	G	93.00	0	NS=1;DP=31
chromosome_2	643391	.	G	T	93.00	0	NS=1;DP=46
chromosome_2	643959	.	A	D1	93.00	0	NS=1;DP=50
chromosome_2	653656	.	A	D1	93.00	0	NS=1;DP=37
chromosome_2	653683	.	T	A	93.00	0	NS=1;DP=37
chromosome_2	653685	.	A	T	93.00	0	NS=1;DP=37
=> chromosome_2	653855	.	.	IA	93.00	0	NS=1;DP=37
chromosome_2	653965	.	T	D1	93.00	0	NS=1;DP=39
chromosome_2	653975	.	A	D1	93.00	0	NS=1;DP=39
chromosome_2	653980	.	T	D1	93.00	0	NS=1;DP=39
chromosome_2	653983	.	C	D1	93.00	0	NS=1;DP=39
chromosome_2	653987	.	T	D1	93.00	0	NS=1;DP=39
chromosome_2	673087	.	.	IT	57.00	0	NS=1;DP=53
chromosome_2	705774	.	.	IA	41.00	0	NS=1;DP=43
chromosome_2	708203	.	T	C	93.00	0	NS=1;DP=50
chromosome_2	713659	.	TA	AT	93.00	0	NS=1;DP=50
chromosome_2	713852	.	T	C	93.00	0	NS=1;DP=50
chromosome_2	723184	.	T	D1	93.00	0	NS=1;DP=32
chromosome_2	773641	.	G	D1	93.00	0	NS=1;DP=41
chromosome_2	773746	.	.	IT	62.00	0	NS=1;DP=41
chromosome_2	827852	.	T	D1	93.00	0	NS=1;DP=31
chromosome_2	876308	.	.	IT	78.00	0	NS=1;DP=49
chromosome_2	927463	.	.	IA	43.00	0	NS=1;DP=33
chromosome_2	964680	.	T	D1	93.00	0	NS=1;DP=41
=> chromosome_2	964692	.	.	ITA	93.00	0	NS=1;DP=41