Is your feature request related to a problem? Please specify.

Clearing previous duplicate settings and tags with samtools markdup shouldn't require that fixmates was run with the mate scoring option.

I just want to remove the duplicate flag so I can run a barcode aware mark duplicate tool.
It would be great if a barcode aware mark duplicate tool would be added to samtools markdup

java -Dpicard.useLegacyParser=false -jar $EBROOTPICARD/picard.jar MarkDuplicates \
        -I "${input_bam_file}" \
        -O "${output_bam_file}" \
        -M "${output_bam_file%.bam}.mark_duplicates_metrics.txt" \
        -BARCODE_TAG CB \
        -REMOVE_DUPLICATES false \
        -OPTICAL_DUPLICATE_PIXEL_DISTANCE 100

broadinstitute/picard#1579