HS.SDA3.GenomicsVariant

Alternate base(s): Comma separated list of alternate non-reference alleles called on at least one of the samples. Options are base strings made up of the bases A,C,G,T,N,* (case insensitive) or an angle-bracketed ID string ("") or a breakend replacement string.

Property methods: ALTDisplayToLogical(), ALTGet(), ALTIsValid(), ALTLogicalToDisplay(), ALTLogicalToOdbc(), ALTNormalize(), ALTSet()

Chromosome: An identifier from the reference genome or an angle-bracketed ID String (") pointing to a contig in the assembly file. No colons or white space permitted

Property methods: CHROMDisplayToLogical(), CHROMGet(), CHROMIsValid(), CHROMLogicalToDisplay(), CHROMLogicalToOdbc(), CHROMNormalize(), CHROMSet()

ID - identifier: Semi-colon separated list of unique identifiers where available. If this is a dbSNP (single nucleotide pair) variant it is encouraged to use the rs number(s). No identifier should be present in more than one data record. TBD: We think these comments mean that CHROM+POS+ID is like a primary key for the row

Position: The reference position, with the 1st base having position 1. It is permitted to have multiple records with the same POS. Telomeres are indicated by using positions 0 or N+1, where N is the lenght of the corresponding chromosome or contig

Quality: Phred-scaled quality score for the assertion made in ALT. i.e. - -10Log10 prob(call in ALT is wrong)

Reference base(s): Each base must be one of A,C,G,T,N (case insensitive). Multiple bases are permitted. The value in the POS field refers to the position of the first base in the String.