Replace picard commands with GATK commands #72
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Do we still want this PR? Or should we add a disclaimer to the tutorial that the commands are pre GATK4? |
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Description
As Picard has been incorporated into GATK from GATK4 onwards, this is a rough substitution of picard commands with GATK commands. It's crucial to note that these modifications have not undergone testing; it is necessary for someone to execute the pipeline to verify that none of the flags have been renamed or altered.
Related issue(s)
Checklist
picardtogatkchanges, in case some of the flag names have been changed in the new version.bioinformatics-workbook/dataAnalysis/VariantCalling/gatk-dnaseq-best-practices-workflow.md
Line 148 in d65bcb9