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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