Q: When using Picard's MarkDuplicates, is it preferable to only mark
duplicates rather than remove them?
A: In our pipelines, we keep the duplicates, as downstream tools can
themselves choose whether to count or discount them in their analysis.
Q: Does the remove duplicates command remove all duplicated reads or does
it leave one representative copy of the read (leaving all unique reads)?
A: It removes all duplicates that would have been marked, leaving a single
representative copy.
Q: If I choose to mark duplicates only, what downstream analyses might this
bias or effect?
A: Depending on the tools, they may not be duplicate aware in their
analysis, meaning they will include them. Other tools in Picard are
duplicate aware, as is the GATK for example.
Q: Generated vcf files shouldn't be compromised by the presence of
duplicates, correct?
A: It depends on the tool you are using to generate the VCF, but generally
most variant callers do not consider the duplicates.
N
On Wed, Nov 19, 2014 at 12:19 AM, Katharine Walter <
katharine.wal...@yale.edu> wrote:
> 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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