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VariantEval Structural Variation

GrantMarshallGrantMarshall Member Posts: 6


I just finished running a fairly large number of WGS samples through HaplotypeCaller and I've been using VariantEval to look at some summary stats on these samples. I've noticed that under '#:GATKTable:VariantSummary:1000 Genomes Phase I summary of variants table' there's a section on structural variations and that apparently I'm getting about 3500 in one of my samples. Here's the actual section of the table in question:

#:GATKTable:VariantSummary:1000 Genomes Phase I summary of variants table
VariantSummary  CompRod  EvalRod  JexlExpression  Novelty  nSamples  nProcessedLoci  nSNPs    TiTvRatio  SNPNoveltyRate  nSNPsPerSample  TiTvRatioPerSample  SNPDPPerSample  nIndels  IndelNoveltyRate  nIndelsPerSample  IndelDPPerSample  nSVs  SVNoveltyRate  nSVsPerSample
VariantSummary  dbsnp    vcf1     none            all             1      3095693981  3446166       2.08            1.34         3446166                2.08             0.0   962028             15.33            962028               0.0  3282          73.58           3282
VariantSummary  dbsnp    vcf1     none            known           1      3095693981  3399907       2.08            0.00         3399907                2.08             0.0   814506              0.00            814506               0.0   867           0.00            867
VariantSummary  dbsnp    vcf1     none            novel           1      3095693981    46259       1.71          100.00           46259                1.71             0.0   147522            100.00            147522               0.0  2415         100.00           2415

I didn't think that HaplotypeCaller even looked for structural variations, so I tried to find these structural variations in the VCF, hoping they were encoded as described here and I couldn't find anything. Could someone tell me why VariantEval is showing a number of structural variations but the actual VCF isn't finding any? Does VariantEval just interpret a sufficiently large indel as a SV? If so, I can understand why it may call some structural variations considering there are indels longer than 1k bp in the indels of the sample.



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