Coverage Metrics Report Example

By default, DRAGEN reports read coverage over the whole genome, and if available also for the target bed. You can specify up to three additional regions over which coverages are reported. In the following example, DRAGEN generates two coverage reports, cov_report and full_res, for the additional coverage region 1.

dragen -f \
-r /staging/human/reference/hg19/hg19.fa.k_21.f_16.m_149 \
-1 /staging/examples/reads/SRA056922_30x_shuffle16k_e10_50M_1.fastq.gz \
-2 /staging/examples/reads/SRA056922_30x_shuffle16k_e10_50M_2.fastq.gz \
--RGID Illumina_RGID \
--RGSM SRA056922_30x_shuffle16k \
--output-directory /staging/examples/ \
--output-file-prefix SRA056922_30x_e10_50M \
--qc-coverage-region-1 /staging/examples/reads/vc_smoke.callable.bed \
--qc-coverage-reports-1 cov_report full_res

The full_res report corresponds to the Bedtools coverage option, and includes a per base resolution read depth. The cov_report includes read depth summaries per region including mean, median, min and max depths.