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Same Sample, Same parameters, significant difference on how the Haplotype caller responds.

NilakshaNilaksha Colombo Sri LankaMember
edited June 2014 in Ask the GATK team

I have been running GATK tools successfully in my pipeline and after the latest addition of gvcf files I used them on my trio variant calling. The problem arose when I used HC to make my gvcfs. First it was a out of memory error, while I was running with 14gig ram and 12 cores. Secondly the problem arose again. And in the third attempt It worked very well. Now the same thing is happening for my next sample. Any body got a clue??? Please do post.
Terminal output has been attached.

Best Answer


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