DRAGEN Enrichment BSSH App

DRAGEN Enrichment is an accurate and efficient end-to-end (FASTQ to VCF) secondary analysis solution for whole exome and targeted panel NGS data; it can be used for both germline and somatic variant calling. This app takes input files in FASTQ, BAM, and CRAM formats. Files may be decompressed, go through Map/Align/Sort, and go through variant calling.

In-run PON support for Germline CNV and Targeted Caller

Version 4.4.4 of the DRAGEN Enrichment BSSH App introduced support for automatic generation of an in-run PON for both CNV calling and the 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).

Use the following steps to run the DRAGEN Enrichment BSSH App on Germline WES data using an in-run PON:

1. Go to version 4.4.4 or later of the DRAGEN Enrichment BSSH App on BaseSpace and click 'Launch Application'.

2. Set the Analysis Name and output Project.

3. Select FASTQs/BAMs/CRAMs for all samples in the sequencing run. At least 5 samples are required for CNV and at least 30 samples are required for Targeted Caller. Input file types cannot be mixed.

4. Make sure 'Variant Caller Mode' is 'Germline' and select a reference. For human samples, select one of the supported pangenome references. Note that Targeted Caller only supports hg38, hg19 and hs37d5.

5. Select the 'Targeted Regions' corresponding to the enrichment protocol for the sequencing run. For Targeted Caller the 'Illumina CS/PGx Custom Enrichment Research Panel' must be used.

6. Expand the 'CNV' section and check the box 'Enable CNV'. For data generated using the Illumina CS/PGx Custom Enrichment Research Panel, check the box 'Enable Targeted Calling'. 'Enable CNV' must be checked before checking the 'Enable Targeted Calling'.

7. Check the box 'Enable In-Run Panel of Normals'.

8. In the field 'In-Run Panel of Normals Excluded Samples' list any samples from the sequencing run that should not be included in the PON. Examples of samples that can be listed here include:

   1. Samples that have not met QC requirements.

   2. Related samples from a large pedigree consisting of more than ~6% of the total number of PON samples (e.g. more than quad for PON of size 50).

   3. Samples that are known to not be copy-neutral in certain target regions of interest and would otherwise make up a large portion of the total PON samples.

9. Expand the 'Advanced Settings' section and set the 'Samples Per Node' field to 5. This value can be increased to reduce the cost overhead for spinning up more nodes, but will increase the total runtime. Decreasing this value will increase the cost overhead, but decrease the total runtime.

10. Click 'Launch Application'.