...you did not provide enough memory to run this program,pooled,haplotypecaller


I am using haplotypecaller version 3.4-46 with pooled data (ploidy 44) and I am running in to the error 'There was a failure because you did not provide enough memory to run this program'. I have a very high coverage (~10000x at each position). Searching in the forums, I have found suggestions of down sampling, (which haplotypecaller does itself in the version I am using) and changing the minPruning parameter (which I am afraid may further compromise the sensitivity of the variant calling given the samples are pooled). Previously I used unifiedgenotyper on the same data and I had no problems. Is there something else I could try to get rid of the memory issues or should I stick with unifiedgenotyper in my case? Thank you for your support.


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    Can you try using the latest version (3.5)? There have been some changes made to the way ploidy calculations are done. I hope that will help solve your problems.


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