markdup

Mark duplicated reads in a BAM/CRAM file.

This tool locates and tags duplicate reads in a BAM or CRAM file, where duplicate reads are defined as originating from a single fragment of DNA.

The input BAM/CRAM must be sorted by queryname. If it is not, run Parabricks bamsort with --sort-order queryname to preprocess the input file. Input BAM/CRAMs must also have at least one read group line.

The behavior of GATK MarkDuplicates differs slightly based on whether its input was coordinate or queryname sorted. By default, markdup matches the output of GATK MarkDuplicates as if it were run with a coordinate-sorted BAM. When using --markdups-assume-sortorder-queryname, markdup matches the output of GATK MarkDuplicates as if it were run with a queryname-sorted BAM.

The Fasta reference input --ref is required for CRAM file support and BAM/CRAM header verification.

Refer to the markdup Reference section for a detailed listing of all available options.

Quick Start

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

Compatible Baseline Command

The commands below are the GATK counterparts of the Parabricks command above. By default, markdup matches the coordinate sort order baseline; however, note that Parabricks markdup requires a queryname sorted input. Use the queryname sort order baseline if running with --markdups-assume-sortorder-queryname. The gatk SortSam commands are included to guarantee the input sort order for MarkDuplicates; they can be skipped if your file is already in the correct order.

Coordinate Sort Order

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gatk SortSam \
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    -R <INPUT_DIR>/${REFERENCE_FILE} \
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    -I <INPUT_DIR>/${INPUT_BAM} \
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    -O <INPUT_DIR>/${SORTED_BAM} \
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    -SO coordinate
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gatk MarkDuplicates \
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    -I <INPUT_DIR>/${SORTED_BAM} \
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    -O <OUTPUT_DIR>/${MARKED_BAM} \
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    -M <OUTPUT_DIR>/${METRICS_FILE} \
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    -ASO coordinate

Queryname Sort Order

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gatk SortSam \
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    -R <INPUT_DIR>/${REFERENCE_FILE} \
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    -I <INPUT_DIR>/${INPUT_BAM} \
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    -O <INPUT_DIR>/${SORTED_BAM} \
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    -SO queryname
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gatk MarkDuplicates \
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    -I <INPUT_DIR>/${SORTED_BAM} \
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    -O <OUTPUT_DIR>/${MARKED_BAM} \
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    -M <OUTPUT_DIR>/${METRICS_FILE} \
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    -ASO queryname
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gatk SortSam \
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    -R <INPUT_DIR>/${REFERENCE_FILE} \
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    -I <OUTPUT_DIR>/${MARKED_BAM} \
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    -O <OUTPUT_DIR>/${FINAL_BAM} \
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    -SO coordinate

Options