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FILTER
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If all filters are passed, PASS is written in the filter column.
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LowDP—Applied to sites with depth of coverage below a cutoff. |
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LowGQ—The genotyping quality (GQ) is below a cutoff. |
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LowQual—The variant quality (QUAL) is below a cutoff. |
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LowVariantFreq—The variant frequency is less than the given threshold. |
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R8—For an indel, the number of adjacent repeats (1-base or 2-base) in the reference is greater than 8. |
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INFO
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Possible entries in the INFO column include:
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AC—Allele count in genotypes for each ALT allele, in the same order as listed. |
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AF—Allele Frequency for each ALT allele, in the same order as listed. |
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AN—The total number of alleles in called genotypes. |
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CD—A flag indicating that the SNP occurs within the coding region of at least 1 RefGene entry. |
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DP—The depth (number of base calls aligned to a position and used in variant calling). |
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EXON—A comma-separated list of exon regions read from RefGene. |
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FC—Functional Consequence. |
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GI—A comma-separated list of gene IDs read from RefGene. |
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QD—Variant Confidence/Quality by Depth. |
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TI—A comma-separated list of transcript IDs read from RefGene. |
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FORMAT
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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:
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AD—Entry of the form X,Y, where X is the number of reference calls, and Y is the number of alternate calls. |
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DP—Approximate read depth; reads with MQ=255 or with bad mates are filtered. |
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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. |
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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. |
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NL—Noise level; an estimate of base calling noise at this position. |
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PL—Normalized, Phred-scaled likelihoods for genotypes. |
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VF—Variant frequency; the percentage of reads supporting the alternate allele. |
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SAMPLE
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The sample column gives the values specified in the FORMAT column.
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