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Small Variants Genome VCF
File name: {Sample_ID}_SmallVariants.genome.vcf
Contains small variant calls for each target coordinate in the TruSight Tumor 170 v1.0 DNA panel.
The following variant call filters are applied during the variant call and filter step.
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Filter Name |
Description |
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Low Variant Quality |
Filtered variant quality score is < 20 (applies to reference and variant allele calls) |
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Low Depth |
Coverage is < 100 for variant calls and < 250 for reference calls |
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Strand Bias |
Strand bias score is ≥ to 0.5 (applies to ALT allele calls only) |
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Low Variant Frequency |
Frequency is < 0.026 (applies to variant allele calls only) |
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Indel Reference Repeat |
Repeat is ≥ to 8 |
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Adjusted Quality |
Baseline quality score is < 10 (applies to ALT allele calls only) |
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Low Variant Support |
Variants with supporting reads < 7 (applies to variant allele calls only) |
If available, variant calls are annotated using the Illumina Annotation Engine with the following information:
| • | HGNC Gene |
| • | Transcript (using the canonical Ensembl transcript) |
| • | Exon (using the canonical Ensembl transcript) |
| • | Consequence (using the canonical Ensembl transcript) |
| • | HGVS Coding Sequence Name (using the canonical Ensembl transcript) |
| • | HGVS Protein Sequence Name (using the canonical Ensembl transcript) |
| • | COSMIC ID |
For Research Use Only. Not for use in diagnostic procedures.