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.