NVIDIA Clara Parabricks Pipelines QC Metrics: BAMMetrics

Accelerated CollectWGSMetrics functionality from GATK4

bammetrics collects whole genome sequencing metrics, similar to CollectWGSMetrics from GATK4, but in a highly accelerated manner. The output metrics match exactly with that of GATK4.

Quick Start


$ pbrun bammetrics --ref Ref.fa --bam wgs.bam --out-metrics-file metrics.txt

Compatible GATK4 Command

The command below is the GATK4 counterpart of the Parabricks command above. The output from these commands will generate the exact same results as the output from the above command.

gatk CollectWGSMetrics -R Ref.fa -I wgs.bam -O metrics.txt




--ref (required)

Path to the reference file.

--bam (required)

Path to the input bam file.

--out-metrics-file (required)

Output metrics file.


Minimum base quality for a base to contribute coverage (default: 20)


Minimum mapping quality for a read to contribute coverage (default: 20)


If true, count unpaired reads, and paired reads with one end unmapped (default: None)


Treat positions with coverage exceeding this value as if they had coverage at this value (but calculate the difference for PCT_EXC_CAPPED) (default: 250)


Defaults to 12.
Number of parallel threads to use.