Picard is flagging dupes, but not actually removing them from BAM.

Should look like this:

picard MarkDuplicates \
    --REMOVE_DUPLICATES true \
    --INPUT /mounts/lovelace/temporary/porter/coreNT_full1/03_sam_sort_coord/1_1_S1.bam \
    --OUTPUT /mounts/lovelace/temporary/porter/coreNT_full1/04_picard_dedupe/1_1_S1.bam \
    --METRICS_FILE /mounts/lovelace/temporary/porter/coreNT_full1/04_picard_dedupe/input-dedupe-stats.txt