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VCF File Headings
Heading |
Description |
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CHROM |
The chromosome of the reference genome. Chromosomes appear in the same order as the reference FASTA file. |
POS |
The single-base position of the variant in the reference chromosome. |
ID |
The rs number for the SNP obtained from dbSNP.txt, if applicable. |
REF |
The reference genotype. For example, a deletion of a single T is represented as reference TT and alternate T. An A to T single nucleotide variant is represented as reference A and alternate T. |
ALT |
The alleles that differ from the reference read. |
QUAL |
A Phred-scaled quality score assigned by the variant caller. |
INFO |
Additional information.String, no white-space, semi-colons, or equals-signs permitted; commas are permitted only as delimiters for lists of values. INFO fields are encoded as a semicolon-separated series of short keys with optional values in the format: <key>=<data>[,data]. |
FORMAT |
If genotype information is present, then the same types of data must be present for all samples. A FORMAT field is given specifying the data types and order (colon-separated alphanumeric String). |
SAMPLE [SAMPLE_ID] |
This is followed by one field per sample, with the colon-separated data in this field corresponding to the types specified in the FORMAT column. |
Within the VCF file headers, descriptions are included for caller specific variant fields.
For Research Use Only. Not for use in diagnostic procedures.