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Hi,Can sambamba replace SortSamSpark for chromosome sorting? Will it affect accuracy?

Hi,Can sambamba replace SortSamSpark for chromosome sorting? Will it affect accuracy?

Answers

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @sailor9527,

    We're not familiar with external tools like sambamba. Given an appropriate Spark cluster setup, my understanding is that GATK Spark tools should outperform their non-Spark counterparts. The scientific results should be equivalent between the versions.

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