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.
$ pbrun bammetrics --ref Ref.fa --bam wgs.bam --out-metrics-file metrics.txt
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
Path to the reference file.
Path to the input bam file.
Output metrics file.
Number of parallel threads to use.