Hi,
When using Picard's MarkDuplicates, is it preferable to only mark
duplicates rather than remove them? Does the remove duplicates command
remove all duplicated reads or does it leave one representative copy of the
read (leaving all unique reads)? If I choose to mark duplicates only, what
downstream analyses might this bias or effect? Generated vcf files
shouldn't be compromised by the presence of duplicates, correct? Although
the fold-coverage at variant sites will be effected depending on whether
you decide to mark or remove.
Thank you very much for your help!
Best,
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