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Nvidia Clara Parabricks fq2bam

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Description

Generate BAM/CRAM output given one or more pairs of FASTQ files. Can also optionally generate a BQSR report.

Publisher

Nvidia

Latest Tag

4.0.0-1

Modified

November 1, 2022

Compressed Size

92.85 MB

Multinode Support

No

Multi-Arch Support

No

4.0.0-1 (Latest) Scan Results

Linux / amd64

fq2bam performs the following steps:

The user can decide to turn-off marking of duplicates. The BQSR step is only performed if the --knownSites input and --out-recal-file output options are provided.

For further information visit the fq2bam help page.

Quick Start

# This command assumes all the inputs are in <INPUT_DIR> and all the outputs go to <OUTPUT_DIR>.
$ docker run --rm --gpus all --volume <INPUT_DIR>:/workdir --volume <OUTPUT_DIR>:/outputdir
    -w /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:<VERSION-TAG> \
    pbrun fq2bam \
    --ref /workdir/${REFERENCE_FILE} \
    --in-fq /workdir/${INPUT_FASTQ_1} /workdir/${INPUT_FASTQ_2}  \
    --knownSites /workdir/${KNOWN_SITES_FILE} \
    --out-bam /outputdir/${OUTPUT_BAM} \
    --out-recal-file /outputdir/${OUTPUT_RECAL_FILE}