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@Sheila said: @jianxinwang Hi, In this thread the team recommends running on 1 interval per sample. In your case, you have 1500 samples, so you would have ~1500 intervals. Looking at the intervals list for hg38 that we provide, it look…
Hi Manolis, I do not know exactly what is the cause for your problem because I used a different command line. However, I would use more RAM to do a test. 4Gb is too small based on my experience. You may also want to experiment using the input g.v…
I asked the same question. Please take a look at this thread: https://gatkforums.broadinstitute.org/gatk/discussion/1975/how-can-i-use-parallelism-to-make-gatk-tools-run-faster The Spark version is still in beta and is not recommended for produc…
I'm having the same problem using v4.0.0. A rerun sometimes can fix the problem. The reason remains unknown.
For GATK4: I don't see multi-threading options for HaplotypeCaller (or any other tools in this version). Is it removed or there are better options? Another question: are there any pipelines available for running GATK on local HPCs using Slurm as job…
Thanks, indeed that is the cause of the problem. My bad!
I'm getting "A USER ERROR has occurred: Invalid argument 'GVCF'." error when running the following command: $ gatk --java-options "-Xmx38000M" HaplotypeCaller -I my_input.bam -R Homo_sapiens_assembly38.fasta -L wgs_calling_regions_chr1.hg38.inter…
I'm having the same problem as of today.