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Set Analysis Parameters

Open Whole Genome Sequencing from BaseSpace Sequence Hub as follows.

Select the Apps tab, and then select Whole Genome Sequencing.

From the Version drop-down list, select 8.0.1.

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 the Select Project button.

Select a project to store app results to, and then select the Select button.

From the Reference Genome drop-down list, select the reference genome you want to reference.

The default reference genome is Human (NCBI GRCh38 PAR-masked with decoys hs38d1).

For input type, select from the following options to specify what the input file type to use.

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Biosample(s) —Analysis is performed from Biosample FASTQ files.

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Aligned BAM(s) —Analysis is performed from aligned BAM files.

Depending on the selected input type, select the Proband data you want to analyze as follows.

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If you selected Biosample for the input type

Select the Select Sample button.

Select the checkbox of the Biosample you want to analyze, and then select a prep kit you want to use with the Biosample.

Select the Select button.

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If you selected Aligned BAM for the input type

Select the Select File button.

Select the checkbox of the BAM file you want to analyze.

Select the Select button.

For variant calling, select from the following options:

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Full analysis–Used to generate calls for small variants, copy number, structural variants, repeat expansions, runs of homozygosity, and variant calls in the SMN and HLA regions. If a trio or a quad is added to the Related Samples section, de novo variants are called.

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Small variants only–Used to generate calls for small variants only.

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None–Variant calling is disabled.

If you selected Aligned BAM(s) for the input type, set the Realign BAMs option.

This setting realigns each input BAM in series, which increases run time and ensures that multiple members of the pedigree have the same alignment and reference genome. Turned on by default.

If your BAMs were generated by a compatible Whole Genome Sequencing app, clear the Realign BAMs checkbox.

[Optional] Expand the Related Samples section and select any additional samples to analyze with the proband.

Joint calling is automatically performed when any samples are specified in this section. If both parents are specified, the Whole Genome Sequencing app performs de novo calling for the proband sample.

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