DRAGEN Germline Enrichment from BCLs BSSH App

DRAGEN Germline Enrichment from BCLs provides accurate and efficient end-to-end (BCL to VCF) germline variant calling of whole exome and targeted panel NGS data. This app takes sequencing output in BCL format, converts them to FASTQs and then performs mapping and variant calling.

In-run PON support for Germline CNV and Targeted Caller

An in-run PON is required for Targeted Caller from WES data (see Targeted Caller | Exome calling), and is the preferred replacement for a pre-built PON for CNV calling (see CNV Preprocessing | Panel of Normals). Given samples from a single sequencing run, the DRAGEN Germline Enrichment from BCLs app will generate the required PON files and use them to analyze each sample in the run. The analysis workflow may be started from a planned run using the Run Planning tool in BSSH or from an existing sequencing run by launching the DRAGEN Germline Enrichment from BCLs app on BSSH. The DRAGEN Germline Enrichment from BCls app does not allow any samples from the sequencing run to be excluded. As a workaround, the DRAGEN BCL Convert Application can be used through Run Planning tool to generate FASTQs and the FASTQs can be used with either the DRAGEN Germline Enrichment ICA app or the DRAGEN Enrichment BSSH app.

DRAGEN Germline Enrichment from BCls through Run Planning Tool

A new run can be configured in BaseSpace Sequence Hub using the Run Planning tool. Follow the steps for your sequencing system described on the Basespace Sequence Hub Help Center | Plan Runs page.

During the configuration stage, use the following steps to configure the run for DRAGEN Germline Enrichment:

1. In the 'Application' field select the desired version under 'DRAGEN Germline Enrichment'

2. Select the appropriate 'Library Prep Kit' for the samples being sequenced. If the Illumina CS/PGx Custom Enrichment Research Panel was used with Exome 2.5 then select 'Illumina DNA Prep with Exome 2.5 Enrichment'.

3. Select the 'Index Adapter Kit' for the samples being sequenced.

4. Click 'Next'.

5. Complete the Analysis Settings section.

6. Click 'Next'.

7. Click 'Save as Planned'.

DRAGEN Germline Enrichment from BCLs from existing run

The DRAGEN Germline Enrichment from BCLs app can run from an existing sequencing run containing BCLs using the steps below.

1. Go to the BaseSpace Sequence Hub Dashboard and click on the 'Apps' tab.

2. In the search bar enter 'DRAGEN Germline Enrichment From BCLs' and click on the app.

3. Make sure the version selected is 4.4.4 or newer and click 'Launch Application'

4. Select the sequencing run containing BCLs

5. If the Sample Sheet in the selected sequencing run is invalid or outdated there may be validation errors. In this case an 'Override Sample Sheet' must be selected. The 'Override Sample Sheet' can be exported from a run created using the Run Planning tool as described above. In the final step of the Run Planning tool, instead of clicking 'Save as Planned', click 'Export' to generate the Override Sample Sheet. Note that the Sample Sheet must first be uploaded to a project on BSSH before it can be selected in the app.

6. Click 'Edit' in the 'Configuration: DRAGEN Germline Enrichment' section.

7. Complete the Analysis Settings section.

8. Click 'Next'.

9. Click 'Requeue' to start the app.

Analysis Settings

Follow the steps below to configure the analysis settings:

1. Select the 'Reference TAR'. For human samples, select one of the supported pangenome references. Note that Targeted Caller only supports hg38, hg19 and hs37d5.

2. Select the 'Panel BED'. If the Illumina CS/PGx Custom Enrichment Research Panel was used, select 'Illumina_Custom_Enrichment_Panel_v2_DRAGEN_Targeted_Calling.<hg38|hg19|hs37d5>.bed'

3. Under 'DRAGEN copy number and targeted calling settings' select the 'In-Run' radio button for the 'CNV Baseline Source' field.

4. If the Illumina CS/PGx Custom Enrichment Research Panel was used select the 'Yes' radio button for the 'Enable targeted paralog calling' field.