Somatic Low Coverage

Input the following command to your local DRAGEN server:

/opt/edico/bin/dragen \
--output-directory ${desired_location} \
--tumor-fastq-list ${fastq-list.csv} \
--ref-dir ${human_ref_v11hashtable} \
--enable-map-align true \
--enable-map-align-output true \
--enable-duplicate-marking true \
--methylation-conversion illumina \
--methylation-generate-cytosine-report=true \
--methylation-compress-cx-report=true \
--enable-variant-caller=true \
--vc-systematic-noise-method=max \
--vc-systematic-noise=${systematic_noise} \
--vc-enable-germline-tagging=true \
--variant-annotation-data=${nirvana_annotations} \
--vc-target-bed=${panel.bed} \
--output-file-prefix=${string} \
--sample-sex auto

OPTIONAL: Append the following to avoid double-counting the coverage of overlapping mate pairs:

--qc-coverage-ignore-overlaps=true

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