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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. |