MatZ
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No, we downloaded and installed GATK locally. For pre-processing/alignment step we used this: https://github.com/gatk-workflows/gatk4-data-processing/archive/master.zip Into the file folder there i...
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That's the point. In the documents there is no mention of an alt file but in the file processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json there is. There are references about all index file...