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Include SAMPLE name in Picard CollectHsMetrics output at runtime?

alanhoylealanhoyle UNC Lineberger Member

When we run the GATK 4.1.x version and earlier of Picard CollectHsMetrics, the last three columns in the initial "METRICS CLASS" data line are SAMPLE, LIBRARY and READ_GROUP, respectively.

Every time I've run this, and I've run this kind of thing literally thousands of times over the years, the last three columns always come back as three blanks.

Is there a way to populate these three values (especially the SAMPLE) at runtime e.g. a command line argument? Or is there another way?

For the record, this is a question I've had simmering since the Picard 1.x days, but i've just recently been asked to combine the HsMetrics outputs in a systematic/automated fashion. It would be super easy if I could just inject the SAMPLE value into that row at runtime. I realize I could do this with a perl/sed/awk/etc one-liner, but if there's an easier way, I'd like to know about it.

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