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Somatic-SNVs-Indels-GATK4 "workspace.intervals" file

Hi! We have WES samples that were analyzed using the Illumina exome capture kit. I have an intervals file (whole_exome_illumina_coding_v1.Homo_sapiens_assembly19.targets.interval_list) which I uploaded into the google bucket for my Somatic-SNVs-Indels-GATK4 workspace. I'm running the Mutect2 workflow, and out of curiosity I launched an analysis on one of my sample pairs in which I 1) designated my Illumina intervals file google bucket link as the attribute for the intervals file in the method config, and 2) where I filled in the "workspace.intervals" attribute for the intervals file variable. I kept everything else the same.

The results in the final MAF are similar but noticeably different when I use my Illumina intervals list vs. the workspace intervals file. I was just wondering what the workspace intervals file corresponds to? Is it meant Illumina or Agilent samples?



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