README.md

enrichment

dragen -f -r ${1} --tumor-fastq1=${2} --tumor-fastq2=${3} \
--RGID-tumor RGID --RGSM-tumor ${4} --output-directory ${5} --output-file-prefix ${4} \
--enable-duplicate-marking true --enable-sort true --output-format BAM --enable-map-align true \
--enable-map-align-output true --enable-bam-indexing true \
--enable-variant-caller true --vc-target-bed=${6} \
--enable-cnv true --cnv-target-bed ${6} --cnv-normals-list ${7} \
--cnv-segmentation-bed ${8} --cnv-segmentation-mode bed \
--cnv-filter-limit-of-detection 0.2 --cnv-filter-length 1000 \
--cnv-enable-gcbias-correction false --cnv-interval-width 100 \
--enable-sv true --sv-call-regions-bed ${6} \
--sv-exome true --sv-use-overlap-pair-envidence true \
--sv-somatic-ins-tandup-hotspot-regions-bed /opt/edico/config/sv_somatic_ins_tandup_hotspot_hg19.bed \
--high-coverage-support-mode true

parameter

/opt/edico/config/sv_somatic_ins_tandup_hotspot_GRCh37.bed
/opt/edico/config/sv_somatic_ins_tandup_hotspot_GRCh38.bed
/opt/edico/config/sv_somatic_ins_tandup_hotspot_hg19.bed

Systematic Noise Filtering

--vc-systematic-noise /path/to/WGS_hg38_v1.0_systematic_noise.bed.gz

Download Prebuilt file: Illumina DRAGEN Systematic Noise Files

Germline filtering

--vc-enable-germline-tagging=true \
--enable-variant-annotation=true \
--variant-annotation-data /path/to/nivarna/ \
--variant-annotation-assembly GRch38

amplicon DNA

dragen -f -r ${1} \
    --tumor-fastq1 ${2} --tumor-fastq2 ${3} \
    --output-directory=${4} --output-file-prefix=${5} \
    --RGID-tumor tumor_RGID --RGSM-tumor ${5} \
    --amplicon-target-bed=${6} \
    --enable-dna-amplicon true --enable-map-align=true \
    --enable-sort=true --enable-map-align-output=true \
    --enable-variant-caller=true \
    --enable-cnv=true \
    --enable-sv=true \
    --vc-use-somatic-hotspots false \
    --amplicon-primer-length 50