roger_d ·

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roger_d
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  • This was very helpful to me, but I needed to make a few changes to get the examples to work: In 2) the required input METRICS_FILE should be added, like this: java -jar MarkDuplicates.jar \ INPUT=sorted_reads.bam \ OUTPUT=dedup_reads.bam …
  • I found the answer myself... create a text file where each line is your "path/to/bam.bam" . and then name it with a ".list" at the end, and then pass it to GATK as -I pathtobams.list.