VCF Input Requirement

Connected Insights imports variant calls for the following variant types in the Variant Call File (VCF) file format (v4.1 and later):

• Small variants (SNVs, MNVs, and small indels)

• Structural variants (SVs)

• Copy number variants (CNVs)

• RNA fusion variants

• RNA splice variants

❗ Imported VCF files must contain at least one sample and be sorted correctly to ensure valid display of results in Connected Insights.

The following sample fields are supported for each variant type:

Small variants

Sample Field	VCF Fields	Details
Allele Depths	AD	The read support for variants called at this position. Expected as a comma separated list of values for the reference allele followed by each alternate allele.
Total Depth	DP	The total read support for all alleles at this position. Will be calculated as the sum of all allele depths if not provided.
Variant Read Frequency / Variant Allele Frequency	VF (or derived from AD)	The proportion of reads supporting each alternate allele. Expected as a comma separated list of values for each alternate allele. Will be calculated based on allele depths and total depth if not provided.
Genotype	GT¹	The genotype of the sample at the given position.

¹ The following GT values are interpreted as an absence of the reported variant and are not imported:

• .

• ./.

• 0

• 0/0

Copy number variants

Requires SVTYPE=CNV in the INFO field of each VCF entry.

Sample Field	VCF Fields	Details
Fold Change	FC, SM	Estimated fold change for the copy number variant.
Copy Number	CN	Estimated absolute copy number for the copy number variant.
Minor-haplotype Copy Number	MCN	Estimated absolute copy number for the minor-haplotype of a copy number variant. When MCN is zero the copy number variant can be determined to be LOH.
Genotype	(Derived from CN when available)¹	The genotype of the sample at the given position.

¹ The following GT values are expected given the CN of the variant:

• 0: The copy number is normal in a region expected to be haploid.

• 1: The copy number differs from normal in a region expected to be haploid.

• 0/0: The copy number is normal in a region expected to be diploid.

• 0/1: The copy number differs from normal and is not a complete loss in a region expected to be diploid.

• 1/1: The copy number is a complete loss in a region expected to be diploid.

Structural variants and RNA fusion variants

Requires SVTYPE=SV (for non-translocation breakends) and SVTYPE=BND (for translocation breakends) in the INFO field of each VCF entry.

Sample Field	VCF Fields	Details
Paired Reads	PR	The paired read support for variants called at this position. Expected as a comma separated list of values for the reference allele followed by each alternate allele.
Split Reads	SR	The split read support for variants called at this position. Expected as a comma separated list of values for the reference allele followed by each alternate allele.
Supporting Reads	(Derived from PR and SR)	The cumulative read support from split reads and paired reads for variants called at this position.
Total Depth	(Derived from PR and SR)	The total reads for all alleles called at this position.
Variant Read Frequency / Variant Allele Frequency	(Derived from PR and SR)	The proportion of reads supporting each alternate allele. Calculated based on supporting reads and total depth.
Genotype	GT¹ (or derived from PR and SR)	The genotype of the sample at the given position.

¹ The following GT values are interpreted as an absence of the reported variant and are not imported:

• .

• ./.

• 0

• 0/0