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Set Analysis Parameters

Open the Tumor Normal app from BaseSpace Sequence Hub as follows.

Select the Apps tab, and then select Tumor Normal.

From the Version drop-down list, select 5.0.0.

Select Launch Application.

To override the default analysis name, enter a preferred analysis name in the Analysis Name field.

The default is the app name with the date and time the session was started.

Select Select Project(s).

In the Select Projects dialog box, select a project to store the app results, and then select the Select button.

From the Reference Genome drop-down list, select from the following options.

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Human (UCSC hg19 PAR-Masked) —The human reference genome is PAR-masked. This means that the Y chromosomes are masked to Ns to avoid mismapping of reads.

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Human (Ensembl GRCh37 PAR-Masked)

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Human (NCBI GRCh38 PAR-Masked with decoys) —The human reference genome has pseudoautosomal regions (PAR) masked and includes versions of autosomes, allosomes, and mitochondria. The reference genome GRCh38 also includes unplaced, unlocalized, and decoy sequences, and the Epstein-Barr virus (EBV).

For Annotation, select from the following options.

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Ensembl —Variants are annotated using Ensembl transcripts.

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RefSeq —Variants are annotated using RefSeq transcripts.

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Both —Variants are annotated using both Ensembl and RefSeq transcripts.

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None —Variants are not annotated.

Select Select AppResult Pairs.

In the Select AppResults Pairs dialog box, select the normal and tumor app results you want to analyze, and then select Confirm.

Sample must be aligned with the Whole Genome Sequencing v 7.0.0 App with the desired reference genome.

Make sure that tumor and normal sample sizes are within the size restrictions. See Workflow Requirements

Select Launch Application to start the analysis.

When the analysis completes, the status of the app session automatically updates, and you receive a confirmation email.

For Research Use Only. Not for use in diagnostic procedures.