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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