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*__Note:__ This pipeline was designed to run on the Triton Shared Compute Cluster (TSCC) at the University of California - San Diego. Running it elsewhere will require modifying the source code.*
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# EnsembleVariantCallingPipeline
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# EnsembleVariantCallingPipeline (v 1.0)
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The EnsembleVariantCallingPipeline takes files in FASTQ or BAM format and performs SNV and INDEL variant calling from 4 variant callers ([Mutect2](https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2), [Strelka2](https://doi.org/10.1038/s41592-018-0051-x), [Varscan2](http://doi.org/10.1101/gr.129684.111), [MuSE](https://doi.org/10.1186/s13059-016-1029-6)) and indel variant calling from 3 variant callers ([Mutect2](https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2), [Strelka2](https://doi.org/10.1038/s41592-018-0051-x), [Varscan2](http://doi.org/10.1101/gr.129684.111)).
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# Pipeline structure

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