Analysis Data

The QC Metrics tab lists QC thresholds and values for each analysis ID in the case. Both failed and complete analysis are shown in the Analysis tab. The most recent analysis will be at the top of the list. For more information about configuring QC thresholds, see Change QC Thresholds

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QC failures for required metrics trigger a QC warning. Clear the warning to enable interpretation. For more information, see Clear a QC Warning.

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QC failures for informational metrics are flagged but do not prevent case interpretation.

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MISSING indicates that the QC metric was not found, either due to a missing threshold in the QC JSON or a missing source metrics file.

The Files tab lists the output directory and select all of the analysis files associated with the case.

A list of all analysis and annotation files can be obtained with the CLI tss files list --path < >.

Select a file to download it. To download files > 5 GB or multiple files at one time, use the CLI tool. For CLI download commands, see Command-Line Interface.

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BAM Files—Aligned sequences and quality scores in the BAM (*.bam) file format.

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VCF Files—Variant calls in the VCF (*.vcf.gz) file format.

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QC Metrics Files—Statistics for each sample and pedigree.

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Visualization Files—Files used to generate tracks in the IGV viewer. For more information about visualization tracks, see IGV Visualizations.

The following files do not exist in the Files tab, but can be downloaded using CLI.

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Genome VCF Files—Variants, references, and no calls for all sites in the genome VCF (gVCF) file format.

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From the Subject Info tab, select Analysis.

2.

Select Download logs.