|
|
|
Genotypes of Interest
If the genotypes of interest feature is turned on (by providing genotypes of interest VCF files), the app produces a VCF file (.genotype.vcf) and a human readable 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 genotypes of interest 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 |
Identifier in the Single Nucleotide Polymorphism Database (dbSNP), a free public archive for genetic variation within and across different species developed and hosted by the National Center for Biotechnology Information (NCBI). |
|
RefAllele |
The reference allele. |
|
AltAllele |
The alt allele. |
|
Filters |
The filters that have been applied to the variant. |
|
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. |
|
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, FORCED_REPORT, or OTHER_CALL. |
|
GenotypeForwardAlleles |
The observed alleles on the forward strands, separated by "/". For example: Ref/Ref, Ref/Alt, Alt/Alt, or NA 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). |
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 following tech note: |
For Research Use Only. Not for use in diagnostic procedures.