Genotypes of Interest
If you provide genotypes of interest VCF files, the app creates a VCF file (*.genotype.vcf) and a CSV file (*.genotype.csv). Each row in the output files represents a variant call of interest (the variant calls or hotspots should be specified in the input VCF files). The fields of the CSV file are defined in the following table.
|
Statistic |
Definition |
|---|---|
|
Chr |
Name of reference chromosome. |
|
Position |
Position within reference chromosome. |
|
ID |
Variant identifier. When Illumina Annotation Engine (IAE) annotation is turned on, the ID is obtained from the ID column of the output genome.vcf file; When IAE annotation is turned off, the ID is obtained from the input genotypes of interest VCF file. |
|
RefAllele |
The reference allele. |
|
AltAllele |
The alt allele. |
|
Filters |
The filters that have been applied to the variant. |
|
GT |
Genotype of the variant following the standard vcf annotation (eg, 0/0, 0/1, 1/1, 2/2 or ./.). |
|
GenotypeText |
Human readable genotype of the variant: REF (reference), HET (heterozygous), HOM (homozygous alternate), NO_CALL, or OTHER_CALL. |
|
GenotypeForwardAlleles |
The observed alleles on the forward strands, separated by "/". eg, Ref/Ref (0/0), Ref/Alt (0/1), Alt/Alt (1/1), or NA (./., 1/2, 2/2) for no call. |
|
GenotypeTopAlleles |
The two single nucleotide alleles on the top strands, concatenated (eg, AT). When TopBotStrand is TOP, GenotypeTopAlleles contains bases in GenotypeForwardAlleles ordered alphabetically; When TopBotStrand is BOT, GenotypeTopAlleles contains complements of the base ordered alphabetically; When TopBotStrand is NA, GenotypeTopAlleles is NA. |
|
TopBotStrand |
Top or bottom strand (ie, TOP, BOT, or NA for indels). See the table below for the strand designation. |
|
Allele1Top |
The first (top) allele in the allele pair GenotypeTopAlleles (A/T/G/C or NA for indels). |
|
Allele2Top |
The second (top) allele in the allele pair GenotypeTopAlleles (A/T/G/C or NA for indels). |
|
VariantQuality |
Phred-scaled quality score indicating how confident we are in this asserted haplotype. |
|
GQ |
Phred-scaled quality score indicating how confident we are in this asserted genotype. |
|
AD |
Number of reads containing the variant allele. |
|
DP |
Number of reads aligned at this position. |
|
VF |
Proportion of the variant allele among all alleles being considered. |
|
GoIFileName |
The name of the input genotypes of interest (GoI) VCF files. If multiple GoI files contain the same variant, the first GoI file name is used. |
The top/bottom strand is determined based on the Ref and Alt alleles in the input genotypes of interest VCF files and the reference genome. The rules are as follows:
| • | If Ref or Alt is not a single nucleotide (eg, indels), then TopBotStrand, Allele1Top, Allele2Top, and GenotypeTopAlleles are set to NA. |
| • | If Ref and Alt are single nucleotides, then the rules are specified in the TOPfollowing tech note: |