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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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artifact_in_normal–TLOD of the normal read set (Normal artifact LOD) exceeds threshold. |
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base_quality–Site filtered because median base quality of alt reads at this locus does not meet threshold. |
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clustered_events–Clustered events observed in the tumor. |
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DRAGENHardQUAL–Applied to sites with QUAL < 10.41 (default cutoff) |
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fragment_length–Site filtered because absolute difference between the median fragment length of alt reads and median fragment length of ref reads at this locus exceeds threshold. |
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germline_risk–Evidence indicates this site is germline, not somatic. |
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lod_fstar–Applied to sites in the mitochondrial contig where lod < 6.3 (default cutoff) |
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low_af–Allele frequency does not meet threshold. |
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LowDepth–Applied to sites with DP ≤1 (default cutoff). |
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mapping_quality–Site filtered because median mapping quality of alt reads at this locus does not meet threshold. |
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multiallelic–Site filtered because more than two alt alleles pass tumor LOD. |
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panel_of_normals–Seen in at least one sample in the panel of normals vcf. |
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PloidyConflict–Applied to sites where the genotype call from the variant caller is not consistent with chromosome ploidy (eg, chrY in Female subjects). |
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read_position–Site filtered because median of distances between start/end of read and this locus exceeds threshold. |
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str_contraction–Site filtered due to suspected PCR error where the alt allele is one repeat unit less than the reference. |
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t_lod–Tumor does not meet likelihood threshold. |
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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–Total number of alleles in called genotypes. |
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DP –Approximate read depth (informative and non-informative); some reads may have been filtered based on mapq, etc. |
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END –Stop position of the interval in gVCF banding. |
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FS –Phred-scaled p-value using Fisher's exact test to detect strand bias. |
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FractionInformativeReads –The fraction of informative reads out of the total reads. |
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LOD –Variant LOD score (for mitochondrial contig). |
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MQ –RMS Mapping Quality. |
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MQRankSum –Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities. |
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QD –Variant Confidence/Quality by Depth. |
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R2_5P_bias–Score based on mate bias and distance from 5 prime end. |
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ReadPosRankSum –Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias. |
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SOR –Symmetric Odds Ratio of 2x2 contingency table to detect strand bias. |
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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—Allele Depth (counting only informative reads out of the total reads) for the ref and alt alleles in the order listed; if the GT is 0/0, the AD is the reference count. If the GT is 0/1 or 1/1, the AD is of the form X,Y, where X is the reference allele count and Y is the alternative allele count. If the GT is 1/2, the AD is of the form Y,Z, where Y and Z are the alternative allele 1 and 2 counts. |
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AF–Allele fractions for alt alleles in the order listed. |
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DP–Approximate read depth (reads with MQ=255 or with bad mates are filtered). |
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F1R2–Count of reads in F1R2 pair orientation supporting each allele. |
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F2R1–Count of reads in F2R1 pair orientation supporting each allele. |
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FT–Sample filter, 'PASS' indicates that all filters have passed for this sample (used in multi-sample VCF). |
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GP–Phred-scaled posterior probabilities for genotypes as defined in the VCF specification. |
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GQ–Phred-scale Genotype Quality. |
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ICNT–Counts of INDEL informative reads based on the reference confidence model. |
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LOD–Per-sample variant LOD score (for mitochondrial contig). |
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MB–Per-sample component statistics to detect mate bias. |
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MIN_DP–Minimum DP observed within the GVCF block. |
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PL–Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification. |
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PRI–Phred-scaled prior probabilities for genotypes. |
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PS–Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group. |
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SB–Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias. |
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SPL–Normalized, Phred-scaled likelihoods for SNPs based on the reference confidence model. |
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SAMPLE
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The sample column gives the values specified in the FORMAT column.
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