text: user180: I am running Picard MarkDuplicates with the following parameters below. On the file described, it takes about 41.6Gb of RAM memory and about 20-25 minutes to compute (only uses 1 core AFAICS).
  java -Xmx54890m -jar picard.jar MarkDuplicates \
      I=/home/dnanexus/in/sorted_bam/TST73-86-2IC_S16_L00.bml.GRCh38.karyo.bam \
      O=./TST73-86-2IC_S16_L00.bml.GRCh38.karyo.deduplicated.bam \
      M=./TST73-86-2IC_S16_L00.bml.GRCh38.karyo.duplication_metrics \
      CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=true
  
  What equivalent free/open source software (samtools?, sambamba?) can I use to obtain the same deduplicated bam file but at a lower cost, considering the instance used here has 8 cores but only one of them is being used, and has about 68Gb of RAM out of which it's using 46Gb odd at peak.
  I think previous versions of samtools/sambamba didn't behave the same way as Picard MarkDuplicates with the parameters above, but I would like to know which recent versions would give me the same output.
  
  user77: As you suggested, sambamba is faster at marking duplicates than picard (it's also multithreaded). Recent versions of samtools have a rewritten duplicate marking algorithm, though I doubt it'll be as quick as sambamba. 46GB of RAM seems excessive for marking duplicates unless you're having it store the whole file in memory.
  
original_text: 180: <p>I am running Picard MarkDuplicates with the following parameters below. On the file described, it takes about 41.6Gb of RAM memory and about 20-25 minutes to compute (only uses 1 core AFAICS).</p>
  
  <pre><code>java -Xmx54890m -jar picard.jar MarkDuplicates \
      I=/home/dnanexus/in/sorted_bam/TST73-86-2IC_S16_L00.bml.GRCh38.karyo.bam \
      O=./TST73-86-2IC_S16_L00.bml.GRCh38.karyo.deduplicated.bam \
      M=./TST73-86-2IC_S16_L00.bml.GRCh38.karyo.duplication_metrics \
      CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=true
  </code></pre>
  
  <p>What equivalent free/open source software (samtools?, sambamba?) can I use to obtain the same deduplicated bam file but at a lower cost, considering the instance used here has 8 cores but only one of them is being used, and has about 68Gb of RAM out of which it's using 46Gb odd at peak.</p>
  
  <p>I think previous versions of samtools/sambamba didn't behave the same way as Picard MarkDuplicates with the parameters above, but I would like to know which recent versions would give me the same output.</p>
   77: <p>As you suggested, sambamba is faster at marking duplicates than picard (it's also multithreaded). Recent versions of samtools have a rewritten duplicate marking algorithm, though I doubt it'll be as quick as sambamba. 46GB of RAM seems excessive for marking duplicates unless you're having it store the whole file in memory.</p>
  