Structural Variant Calling Examples

Structural Variant calling can run in the following modes:

•

Standalone—Runs from mapped BAM/CRAM input files. Requires the ‑‑enable‑map‑align=false and --enable-sv=true options.

•

Integrated—Automatically runs on the output of the DRAGEN mapper/aligner. Requires the ‑‑enable‑map‑align=true, --enable-sv=true, and --enable-map-align-output=true options.

Structural Variant calling can be enabled along with any other caller as well.

Integrated Execution Example

dragen -f \
--ref-dir <HASH_TABLE_DIR> \
--enable-map-align true \
--enable-map-align-output true \
--enable-sv true \
--output-directory <OUT_DIR> \
--output-file-prefix <PREFIX> \
-1 <FASTQ1> -2 <FASTQ2> \
--RGID <RGID> \
--RGSM <RGSM>

Standalone Joint Diploid Calling Example

dragen -f \
--ref-dir <HASH_TABLE_DIR> \
--enable-map-align false \
--enable-sv true \
--bam-input <BAM1> \
--bam-input <BAM2> \
--bam-input <BAM3> \
--output-directory <OUT_DIR> \
--output-file-prefix <PREFIX>

Standalone De Novo Quality Scoring Example

dragen -f \
--variant <TRIO_VCF_FILE> \
--pedigree-file <PED_FILE> \
--enable-map-align false \
--sv-denovo-scoring true \
--output-directory <OUT_DIR> \
--output-file-prefix <PREFIX>