LG
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LG commented,
I also got this error. The way to make it work is to throw three slashes after gendb:, like "-V gendb:///home/your db path".
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LG commented,
@danilovkiri , thanks for the comment. So as a short answer, the raw reads should be checked by fastqc and trimmed for adapters before entering GATK pipeline?
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LG created a post,
Do I need to perform fastqc and adapters trimming before gatk pipeline?
Dear Community, I guess this is a pretty straightforward simple question. Do I need to perform fastqc and adapters trimming before gatk pipeline? I have asked around and got controversy answers.