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GATK depth of coverage

I am calculating the Depth of coverage for 100 samples using the following command
java -Xmx20g -XX:ParallelGCThreads=20 -jar /mnt/exome/Softwares/GenomeAnalysisTK.jar -T DepthOfCoverage -I BAMaa.list -L /mnt/exome/Softwares/HG19/nexterarapidcapture_exome_target_region.bed -R /mnt/exome/ReferenceFiles/human_g1k_v37.fasta -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o group1.data

After running till chr 11, I got an error as follows ##### ERROR ------------------------------------------------------------------------------------------

ERROR A USER ERROR has occurred (version 3.6-0-g89b7209):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: An error occurred because you did not provide enough memory to run this program. You can use the -Xmx argument (before the -jar argument) to adjust the maximum heap size provided to Java. Note that this is a JVM argument, not a GATK argument.
ERROR ------------------------------------------------------------------------------------------

I have used -Xmx20g. Anyone can give me a suggestion regarding how I should use -Xmx in case of 100 samples. I used the same command for 30 samples it ran perfectly. Looking forward to hear from you as soon as possible.

Thanks and Regards
Neethu

Answers

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