The current GATK version is 3.8-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Got a problem?

1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?

Then follow instructions in Article#1894.

Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Download the latest Picard release at
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

Picard tools MarkDuplicates without swap usage

I've been trying to run MarkDuplicates on a shared cluster and I keep getting the job killed because of swap usage. I'm trying to figure out a way to use MarkDuplicates without just throwing tonnes of ram at it. To get more ram, I need to request more cores which means lower priority in the queuing system.

I've been using the command:
java -Xmx40g -Djavaio.tmpdir=/home/gowens/tmp -jar $picard MarkDuplicates I=${name}.bam O=${name}.dup.bam M=${name}.dupmetrics.txt CREATE_INDEX=TRUE TMP_DIR=/home/gowens/tmp MAX_RECORDS_IN_RAM=5000000;

I've tried changing MAX_RECORDS_IN_RAM up or down but I'm not sure if thats helping or hurting the problem. For reference, the BAM files I'm marking are 2G to 23G in size and the issue is with the ones on the larger size.

Issue · Github
by Sheila

Issue Number
Last Updated
Closed By


Sign In or Register to comment.