This recipe is for processing whole exome sequencing data for germline workflows.
For most scenarios, simply creating the union of the command line options from the single caller scenarios will work.
Configure the INPUT options
Configure the OUTPUT options
Configure MAP/ALIGN depending on if realignment is desired or not
Configure the VARIANT CALLERs based on the application
Configure any additional options
Build up the necessary options for each component separately, so that they can be re-used in the final command line.
The following are partial templates that can be used as starting points. Adjust them accordingly for your specific use case.
Optional settings per component are listed below. Full option list at this page.
Please include the matched normal sample in the CNV panel of normals.
Generating Panel of Normals (PON)
WES CNV requires PON files. Follow the two steps below to generate CNV PON:
Target counts generation (per normal sample): Target counts of individual normal sample should be generated as baseline. Any options used for panel of normals generation (BED file, GC Bias Correction, etc) should be matched when processing the case sample.
Combined counts generation: Individual PON counts can be merged into a single file as a <prefix>.combined.counts.txt.gz
file.
$CNV_NORMALS_LIST
is a single text file with paths to each target counts file generated by step1 (either .target.counts.gz
or .target.counts.gc-corrected.gz
). Output will have a PON file with suffix .combined.counts.txt.gz
file. Use the PON file in case sample runs of DRAGEN CNV with --cnv-combined-counts
option.
For more information, see Panel of Normals.
Option | Description |
---|---|
Option | Description |
---|---|
--cnv-enable-gcbias-correction true
Enable or disable GC bias correction when generating target counts. For more information, see GC Bias Correction.
enable-hla
Enable HLA typer (this setting by default will only genotype class 1 genes)
hla-enable-class-2
Extend genotyping to HLA class 2 genes