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haplotypecaller step took unusual long time

Hi, I have been using the best practices pipeline for illumnia samples for quite long time. Everything is fine.
Recently, I am using the same pipeline for IONTORRENT samples. Everything is fine until the haplotypecaller step.
I only got two samples to do the haplotypecaller. One bam file is around 9G, and the other is around 13G. But the speed of this step is really slow. It need around 24 weeks to finish haplotypecaller step. It's really strange. Cause if I run the haplotypecaller for a family with 9 persons (Illumina), it only took around 9 days to finish it. How come these two files would need 24 weeks. Does anyone have any idea about what may cause this problem? The bam file of those 9 person are around the same size of the two IONTORRENT samples.

Thank you.

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  • zhoujiayizhoujiayi CanadaMember

    Thank you very much. So the best practice pipeline is only suitable for Illumina samples?

  • zhoujiayizhoujiayi CanadaMember
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