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

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.

--minimum-base-quality

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

--minimum-mapping-quality

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

--count-unpaired

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

--coverage-cap

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)

--num-threads

Defaults to 12.
Number of parallel threads to use.