markdup - NVIDIA Docs

Mark duplicated reads in a BAM/CRAM file.

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

markdup supports the marking of duplicates in two ways, assuming the sort order to be coordinate (the default) or queryname (--markdups-assume-sortorder-querynamer).

The input BAM/CRAM must be sorted by queryname. If it is not, please run pbrun bamsort with --sort-order queryname to preprocess the input file.

Quick Start

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            # 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 \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.3.1-1 \
    pbrun markdup \
    --ref /workdir/${REFERENCE_FILE} \
    --in-bam /workdir/${INPUT_BAM} \
    --out-bam /outputdir/${OUTPUT_BAM}

The command below is the GATK counterpart of the Parabricks command above. Note that the corresponding baseline command is different between marking by coordinate and by queryname. Choose the correct one based on your case. The first gatk SortSam command is listed here to guarantee the order of the input file to MarkDuplicates. Feel free to ignore it if your file order is correct.

Coordinate Sort Order

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            gatk SortSam \
    -R <INPUT_DIR>/${REFERENCE_FILE} \
    -I <INPUT_DIR>/${INPUT_BAM} \
    -O <INPUT_DIR>/${SORTED_BAM} \
    -SO coordinate

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

Queryname Sort Order

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            gatk SortSam \
    -R <INPUT_DIR>/${REFERENCE_FILE} \
    -I <INPUT_DIR>/${INPUT_BAM} \
    -O <INPUT_DIR>/${SORTED_BAM} \
    -SO queryname

gatk MarkDuplicates \
    -I <INPUT_DIR>/${SORTED_BAM} \
    -O <OUTPUT_DIR>/${MARKED_BAM} \
    -M <OUTPUT_DIR>/${METRICS_FILE} \
    -ASO queryname

gatk SortSam \
    -R <INPUT_DIR>/${REFERENCE_FILE} \
    -I <OUTPUT_DIR>/${MARKED_BAM} \
    -O <OUTPUT_DIR>/${FINAL_BAM} \
    -SO coordinate

markdup Reference

Mark duplicate reads in BAM file. The input file should be sorted by queryname.

Input/Output file options

--in-bam IN_BAM
--out-bam OUT_BAM
--ref REF
--out-duplicate-metrics OUT_DUPLICATE_METRICS

Tool Options:

--markdups-assume-sortorder-queryname
--optical-duplicate-pixel-distance OPTICAL_DUPLICATE_PIXEL_DISTANCE

Performance Options:

--num-zip-threads NUM_ZIP_THREADS
--num-worker-threads NUM_WORKER_THREADS
--mem-limit MEM_LIMIT

Common options:

--logfile LOGFILE
--tmp-dir TMP_DIR
--with-petagene-dir WITH_PETAGENE_DIR
--keep-tmp
--no-seccomp-override
--version

GPU options:

--num-gpus NUM_GPUS