Hey Ryan,
my apologies for the late response, and in case you haven't resolved the
issue, I have the following clarification.
You may be using the LIBRARY incorrectly by having the same value across
multiple samples. Even in the case of a pool, having different library
identifiers is preferred. In the corrected case you will get the intended
behavior,
N
On Mon, Oct 13, 2014 at 2:59 PM, Ryan G <ngsbioinformat...@gmail.com> wrote:
> All the picard tools output metrics by ALL_READS, SAMPLE, LIBRARY, and
> READ_GROUP. MarkDuplicates does not do this. It only outputs by LIBRARY.
>
> I'm tying to use the case where my samples have unique SAMPLE and prepared
> with the same LIBRARY. When I use CollectAlignmentMetrics, the output is
> organized by SAMPLE, with the LIBRARY string being the same.
>
> When I merge the output of MarkDuplicates however, SAMPLE is missing and
> there is no way to tell the different between samples as LIBRARY is the
> same.
>
> How are other people handling this? Is it possible to add
> METRIC_ACCUMULATION_LEVEL flag to MarkDuplicates or output the SAMPLE read
> group info as a column?
>
>
>
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