CNV Variant Calling - Human

Input the following command to your local DRAGEN server:

/opt/edico/bin/dragen \
--output-directory ${desired_location} \
--fastq-list ${fastq-list.csv} \
--ref-dir ${human_ref_v11hashtable} \
--enable-map-align true \
--enable-map-align-output true \
--enable-duplicate-marking true \
--methylation-conversion illumina \
--methylation-generate-cytosine-report=true \
--methylation-compress-cx-report=true \
--enable-variant-caller=true \
--enable-cnv=true \
--enable-sv=true \
--enable-sv-cnv=true \
--cnv-enable-self-normalization=true \
--output-file-prefix=${string} \
--vc-emit-ref-confidence GVCF

Note: Update the ${text} fields with the parameter specified