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, please 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.

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

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

            

            
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

            

            
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
        

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