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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 6.0.0.

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.

In the Select Project 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 pseudoautosomal regions of the Y chromosome 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 Normal alignment, select Select Dataset File(s).

The label of this button in the software interface might be different from the label in this guide, depending on the BaseSpace™ Sequence Hub mode.

In the Select Dataset File(s), select the BAM file for the normal input.

Only BAM files that have been generated by Whole Genome Sequencing v8 are shown.

For Tumor alignment, select Select Dataset File(s).

In the Select Dataset File(s), select the BAM file for the tumor input.

Only BAM files that have been generated by Whole Genome Sequencing v8 are shown.

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.

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