Analysis Output | Output Files | VCF File Format

VCF File Format

Variant Call Format (VCF) is a widely used file format developed by the genomics scientific community that contains information about variants found at specific positions in a reference genome.

Table 1 VCF Headings Table
Heading	Description
CHROM	The chromosome of the locus.
POS	The positional coordinate of the locus.
REF	The reference base for the POS and can only be A, C, T, G, or N.
ALT	The called base for the POS and can only be A, C, T ,G ,N, period (.), or asterisk (). The asterisk () is used when there is a deletion at the locus of an upstream POS.
QUAL	The field is not used.
FILTER	PASS—For a called position NoData—For a position without coverage.
INFO	The field is not used.
FORMAT	The field contains the key name for the information on each reported attribute in the SAMPLE column. The keys are colon-separated and reference the #FORMAT descriptors in the header of the file.
SAMPLE	The field contains the values for each field from the FORMAT column.