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Test-drive the GATK tools and Best Practices pipelines on Terra
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the importance of sorting markduplicate output files
I discovered that several outputfiles from "markduplicates" (picard) was sent on in the "best-practice workflow (GATK4.1) " without sorting through BaseRecalibrator, BQSR (gatk ApplyBQSR) and Haplotypecaller to make g.vcf files of each sample. No obvious problems or error msg. The plan is to combine these one in a common vcf-file for variant calling. Is there a need to rerun and get these samples (coordinate) sorted after markduplicates and then rerun BaseRecalibrator, ApplyBQSR and Haplotypecallerto avoid errors?