Somatic Small Variant Caller Examples

If you are using the Tumor-Normal BAM input option, and your BAM read groups have a shared RGID, DRAGEN cannot determine which read group the reads belong to. Ideally, you should have different RGIDs for each read group, but you can work around the problem by setting the ‑‑prepend-filename-to-rgid to true.

Paired-End FASTQ Input

dragen -f \
-r /staging/human/reference/hg19/hg19.fa.k_21.f_16.m_149 \
--tumor-fastq1 /staging/examples/reads/SRA056922_30x_shuffle16k_e10_50M_1.fastq.gz \
--tumor-fastq2 /staging/examples/reads/SRA056922_30x_shuffle16k_e10_50M_2.fastq.gz \
--enable-variant-caller true \
--RGID-tumor DRAGEN_RGID \
--RGSM-tumor DRAGEN_RGSM \
--output-directory /staging/examples/ \
--output-file-prefix SRA056922_30x_e10_50M

Sorted BAM Input

dragen -f \
-r /staging/human/reference/hg19/hg19.fa.k_21.f_16.m_149 \
--tumor-bam-input /staging/examples/SRA056922_30x_e10_50M.bam \
--enable-variant-caller true \
--output-directory /staging/examples/ \
--output-file-prefix sorted_output_SRA056922_30x_e10_50M \
--enable-map-align false \
--prepend-filename-to-rgid true