Small Variants Genome VCF
File name: {Sample_ID}_SmallVariants.genome.vcf
This file contains small variant calls for each target coordinate in the TruSight Tumor 170 v2.0 DNA panel.
The following variant call filters are applied during the variant call and filter step.
|
Filter Name |
Description |
|---|---|
|
Low Quality |
Quality score is < 20 (applies to reference and variant allele calls). |
|
Low Depth |
Coverage is < 100 for variant calls and < 250 for reference calls. |
|
Strand Bias |
Strand bias score is ≥ to 0.5 (applies to variant allele calls only). |
|
Low Variant Frequency |
Frequency is < 0.02 (applies to variant allele calls only). |
|
Indel Reference Repeat |
Partial or total repeats of the variant allele (max repeat length 5) in the reference are ≥ 9 (applies to insertion and deletion variant calls only). |
|
Adjusted Quality |
Baseline quality score is < 10 (applies to variant allele calls only). |
|
Low Variant Support |
Variants with supporting reads < 7 (applies to variant allele calls only). |