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

CLI
$ 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

Options

Option

Description

--ref

(required)

Path to the reference file.

--bam

(required)

Path to the input bam file.

--out-metrics-file

(required)

Output metrics file.

--num-threads

Defaults to 12.

Number of parallel threads to use.