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Change QC Thresholds

TruSight Software evaluates QC metrics for sample data in the case. You can change the default QC thresholds in test configurations for FASTQ variant analysis.

If a sample fails to meet all QC thresholds, TruSight Software assigns the QC Warning label. You cannot interpret the case until the warning is cleared or the case is modified.

For more information about QC metrics and QC warnings, see Analysis Data.

1. In a Draft test, select the Variant Analysis - From FASTQ analysis pipeline.

The current QC thresholds are listed in the QC Threshold field.

2. Modify threshold values. Thresholds cannot be added or deleted.
3. Select Validate.
4. If validation fails, correct the errors or select Reset to Default to clear all changes.
ClosedQC Metrics

TruSight Software uses mapping, gender, and pedigree QC metrics from PAS analysis.

QC Metric

Definition

Percent autosome callability

The percent of non-N reference positions having a passing genotype call in targeted regions of autosomal chromosomes.

Average autosomal coverage over genome

Total number of bases that aligned to autosomes (or to the autosomal loci in the target region) divided by the total number of loci in the autosomes (or to the autosomal loci in the target region). If there was no autosome in the reference genome, this metric shows as NA.

AT dropout

The measurement of AT undercoverage relative to the mean.

GC dropout

The measurement of GC undercoverage relative to the mean.

Normalized coverage at GCs 81-100

The normalized coverage over the GC content range 81–100.

Estimated sample contamination

The percentage of reads in a sample that may be from another human source.

This metric is not included in the default QC thresholds. To include the metric, add the following line to the QC Thresholds when creating the test:

Estimated sample contamination, upper threshold: <percent>

where <percent> is the upper threshold percent.

Insert length median

Median length of the sequenced fragment. The fragment length is calculated based on the locations at which a read pair aligns to the reference.The read mapping information is parsed from the BAM files.

Mapped reads

The total number of mapped reads minus the number of unmapped reads.

Paired reads mapped to different chromosomes (MAPQ > 10)

The number of reads with MAPQ > 10 that have a mate mapped to a different chromosome.

Q30 bases

The percentage of bases with a 30 or above quality score.

Q30 bases R1

The percentage of Read 1 bases with a 30 or above quality score.

Q30 bases R2

The percentage of Read 2 bases with a 30 or above quality score.

Mismatched bases R1

The percentage of unique aligned Read 1 bases where the Read 1 base is different than the reference base.

Mismatched bases R2

The percentage of unique aligned Read 2 bases where the Read 2 base is different than the reference base.

Percent SNVs in large ROH (≥ 3 Mb)

The percentage of SNVs in a sample that occur in regions of homozygosity larger than three megabases.

Sex ploidy validation

The sex of the subject matches the predicted sex from the analysis.

This QC check is optional. To perform analysis without the check, set the QC Threshold test parameter value to false.

SNV Het/hom ratio

The ratio of the number of heterozygous SNPs and number of homozygous SNPs detected for the sample.

Ti/Tv ratio

The ratio of transitions and transversions in SNPs.

• Transitions are variants of the same nucleotide type (pyrimidine to pyrimidine, C and T; or purine to purine, A and G).
• Transversions are variants of a different nucleotide type (pyrimidine to purine, or purine to pyrimidine).

Trio concordance

The percentage of non-de novo SNPs computed by the concordance check for the proband.

This QC check is optional. To perform analysis without the check, set the QC Threshold test parameter value to false.