VCF INFO Fields

ID	Description
IMPRECISE	Flag indicating that the structural variation is imprecise, ie, the exact breakpoint location is not found
SVTYPE	Type of structural variant
SVLEN	Difference in length between REF and ALT alleles
END	End position of the variant described in this record
CIPOS	Confidence interval around POS
CIEND	Confidence interval around END
CIGAR	CIGAR alignment for each alternate indel allele
MATEID	ID of mate breakend
EVENT	ID of event associated to breakend
HOMLEN	Length of base pair identical homology at event breakpoints
HOMSEQ	Sequence of base pair identical homology at event breakpoints
SVINSLEN	Length of insertion
SVINSSEQ	Sequence of insertion
LEFT_SVINSSEQ	Known left side of insertion for an insertion of unknown length
RIGHT_SVINSSEQ	Known right side of insertion for an insertion of unknown length
PAIR_COUNT	Read pairs supporting this variant where both reads are confidently mapped
BND_PAIR_COUNT	Confidently mapped reads supporting this variant at this breakend (mapping may not be confident at remote breakend)
UPSTREAM_PAIR_COUNT	Confidently mapped reads supporting this variant at the upstream breakend (mapping may not be confident at downstream breakend)
DOWNSTREAM_PAIR_COUNT	Confidently mapped reads supporting this variant at this downstream breakend (mapping may not be confident at upstream breakend)
BND_DEPTH	Read depth at local translocation breakend
MATE_BND_DEPTH	Read depth at remote translocation mate breakend
JUNCTION_QUAL	If the SV junction is part of an EVENT (ie, a multi-adjacency variant), this field provides the QUAL value for the adjacency in question only
SOMATIC	Flag indicating a somatic variant
SOMATICSCORE	Somatic variant quality score
JUNCTION_SOMATICSCORE	If the SV junction is part of an EVENT (ie, a multi-adjacency variant), this field provides the SOMATICSCORE value for the adjacency in question only
CONTIG	Assembled contig sequence, if the variant is not imprecise (with ‑‑outputContig)
DUPSVLEN	Length of duplicated reference sequence
DUPHOMLEN	Length of base pair identical homology at event breakpoints excluding duplicated reference sequence
DUPHOMSEQ	Sequence of base pair identical homology at event breakpoints excluding duplicated reference sequence
DUPSVINSLEN	Length of inserted sequence after duplicated reference sequence
DUPSVINSSEQ	Inserted sequence after duplicated reference sequence
NotDiscovered	Variant candidate specified by the user and not discovered from input sequencing data
UserInputId	Variant ID from user input VCF
KnownSVScoring	Variant is associated with a user specified input variant, therefore scoring and filtration criteria are relaxed under a stronger prior assumption of truth

IMPRECISE

Flag indicating that the structural variation is imprecise, ie, the exact breakpoint location is not found

SVTYPE

Type of structural variant

SVLEN

Difference in length between REF and ALT alleles

END

End position of the variant described in this record

CIPOS

Confidence interval around POS

CIEND

Confidence interval around END

CIGAR

CIGAR alignment for each alternate indel allele

MATEID

ID of mate breakend

EVENT

ID of event associated to breakend

HOMLEN

Length of base pair identical homology at event breakpoints

HOMSEQ

Sequence of base pair identical homology at event breakpoints

SVINSLEN

Length of insertion

SVINSSEQ

Sequence of insertion

LEFT_SVINSSEQ

Known left side of insertion for an insertion of unknown length

RIGHT_SVINSSEQ

Known right side of insertion for an insertion of unknown length

PAIR_COUNT

Read pairs supporting this variant where both reads are confidently mapped

BND_PAIR_COUNT

Confidently mapped reads supporting this variant at this breakend (mapping may not be confident at remote breakend)

UPSTREAM_PAIR_COUNT

Confidently mapped reads supporting this variant at the upstream breakend (mapping may not be confident at downstream breakend)

DOWNSTREAM_PAIR_COUNT

Confidently mapped reads supporting this variant at this downstream breakend (mapping may not be confident at upstream breakend)

BND_DEPTH

Read depth at local translocation breakend

MATE_BND_DEPTH

Read depth at remote translocation mate breakend

JUNCTION_QUAL

If the SV junction is part of an EVENT (ie, a multi-adjacency variant), this field provides the QUAL value for the adjacency in question only

SOMATIC

Flag indicating a somatic variant

SOMATICSCORE

Somatic variant quality score

JUNCTION_SOMATICSCORE

If the SV junction is part of an EVENT (ie, a multi-adjacency variant), this field provides the SOMATICSCORE value for the adjacency in question only

CONTIG

Assembled contig sequence, if the variant is not imprecise (with ‑‑outputContig)

DUPSVLEN

Length of duplicated reference sequence

DUPHOMLEN

Length of base pair identical homology at event breakpoints excluding duplicated reference sequence

DUPHOMSEQ

Sequence of base pair identical homology at event breakpoints excluding duplicated reference sequence

DUPSVINSLEN

Length of inserted sequence after duplicated reference sequence

DUPSVINSSEQ

Inserted sequence after duplicated reference sequence

NotDiscovered

Variant candidate specified by the user and not discovered from input sequencing data

UserInputId

Variant ID from user input VCF

KnownSVScoring

Variant is associated with a user specified input variant, therefore scoring and filtration criteria are relaxed under a stronger prior assumption of truth