Analysis Output | Output Files | VCF File Format | VCF File Annotations

VCF File Annotations

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Description

FILTER

If all filters are passed, PASS is written in the filter column.

• LowDP—Applied to sites with depth of coverage below a cutoff.
• LowGQ—The genotyping quality (GQ) is below a cutoff.
• LowQual—The variant quality (QUAL) is below a cutoff.
• LowVariantFreq—The variant frequency is less than the given threshold.
• R8—For an indel, the number of adjacent repeats (1-base or 2-base) in the reference is greater than 8.
• SB—The strand bias is more than the given threshold. Used with the Somatic Variant Caller and GATK.

INFO

Possible entries in the INFO column include:

• AC—Allele count in genotypes for each ALT allele, in the same order as listed.
• AF—Allele Frequency for each ALT allele, in the same order as listed.
• AN—The total number of alleles in called genotypes.
• CD—A flag indicating that the SNP occurs within the coding region of at least 1 RefGene entry.
• DP—The depth (number of base calls aligned to a position and used in variant calling).
• Exon—A comma-separated list of exon regions read from RefGene.
• FC—Functional Consequence.
• GI—A comma-separated list of gene IDs read from RefGene.
• QD—Variant Confidence/Quality by Depth.
• TI—A comma-separated list of transcript IDs read from RefGene.

FORMAT

The format column lists fields separated by colons. For example, GT:GQ. The list of fields provided depends on the variant caller used. Available fields include:

• AD—Entry of the form X,Y, where X is the number of reference calls, and Y is the number of alternate calls.
• DP—Approximate read depth; reads with MQ=255 or with bad mates are filtered.
• GQ—Genotype quality.
• GQX—Genotype quality. GQX is the minimum of the GQ value and the QUAL column. In general, these values are similar; taking the minimum makes GQX the more conservative measure of genotype quality.
• GT—Genotype. 0 corresponds to the reference base, 1 corresponds to the first entry in the ALT column, and so on. The forward slash (/) indicates that no phasing information is available.
• NL—Noise level; an estimate of base calling noise at this position.
• PL—Normalized, Phred-scaled likelihoods for genotypes.
• SB—Strand bias at this position. Larger negative values indicate less bias; values near 0 indicate more bias. Used with the Somatic Variant Caller and GATK.
• VF—Variant frequency; the percentage of reads supporting the alternate allele.

SAMPLE

The sample column gives the values specified in the FORMAT column.