VCF format

Header

Fileformat: We use VCF 4.3.

##fileformat=VCFv4.3

TODO

##filedate TODO

Source: Our Caller with current version:

##source=iGenVarCallerV0.0.3

Contig: IDs of chromosomes and their length

##contig=<ID=chr1,length=482>

Info: In the INFO column we add the information about SVTYPE, SVLEN, END.

##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of SV called.",Source="iGenVarCaller",Version="1.0">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of SV called.",Source="iGenVarCaller",Version="1.0">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of SV called.",Source="iGenVarCaller",Version="1.0">

ALT (Alternative allele field format): Structural Variants

##ALT=<ID=CNV,Description="Copy number variable region">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=DUP:TANDEM,Description="Tandem Duplication">
##ALT=<ID=INS,Description="Insertion of novel sequence">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=TRA,Description="Translocation">

FORMAT (Individual format field format): Genotype field

##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

Body

Deletion

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	MYSAMPLE
chr1	57	.	N	<DEL>	.	PASS	END=70;SVLEN=-13;SVTYPE=DEL	GT	./.