> For clean Markdown of any page, append .md to the page URL.
> For a complete documentation index, see https://docs.nvidia.com/clara/parabricks/llms.txt.
> For AI client integration (Claude Code, Cursor, etc.), connect to the MCP server at https://docs.nvidia.com/clara/parabricks/_mcp/server.

# collectmultiplemetrics

Run a GPU-accelerated version of GATK’s CollectMultipleMetrics.

This tool applies an accelerated version of the GATK CollectMultipleMetrics for assessing BAM
file metrics such as alignment success, quality score distributions, GC bias, and sequencing
artifacts. This functions as a ‘meta-metrics’ tool that can run
any combination of the available metrics tools in GATK to perform an overall assessment
of how well a sequencing run has been performed. The available metrics
tools (PROGRAMs) can be found in the reference section below.

Refer to the [collectmultiplemetrics Reference](#options) section for a detailed listing of all available options.

## Quick Start

```sh
# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1 \
    pbrun collectmultiplemetrics \
    --ref /workdir/${REFERENCE_FILE} \
    --bam /workdir/${INPUT_BAM} \
    --out-qc-metrics-dir /outputdir/${OUTPUT_DIR}\
    --gen-all-metrics
```

## Compatible GATK4 Command

The command below is the GATK4 counterpart of the Parabricks command above. The output
from this command will be identical to the output from the above command.

```sh
$ gatk CollectMultipleMetrics \
--REFERENCE_SEQUENCE <INPUT_DIR>/${REFERENCE_FILE} \
-I <INPUT_DIR>/${INPUT_BAM} \
-O <OUTPUT_DIR>/${OUTPUT_DIR} \
--PROGRAM CollectAlignmentSummaryMetrics \
--PROGRAM CollectInsertSizeMetrics \
--PROGRAM QualityScoreDistribution \
--PROGRAM MeanQualityByCycle \
--PROGRAM CollectBaseDistributionByCycle \
--PROGRAM CollectGcBiasMetrics \
--PROGRAM CollectSequencingArtifactMetrics \
--PROGRAM CollectQualityYieldMetrics
```

## Options