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Analyzing Bismark / Bowtie alignments with GATK (Hard vs Soft clipped data)

JonRJonR IndianaMember

GATK team, is it ok to use GATK on BISMARK alignments? Given the caveats below? This is straight from the developers at babraham.ac.uk

"In contrast to tools like GATK which specifically ask you not to perform any quality trimming up-front but rather use soft clipping during the alignment step, Bismark is designed to to be used only with properly adapter and base call quality trimmed data (Trim Galore uses a Phred score cut-off of 20 by default). Because of this additional step we do not check the basecall quality again during the extraction process."

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