Provide a bait file to Picard's CollectHsMetrics #3695
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Allow the ``bait_regions`` in the datadict, so that a path to a BED file can be specified. This will eventually be passed picard's CollectHsMetrics. (This part is not yet implemented).
Retrieve the bait_regions file from the datadict, and passed it on to picard.
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Hi!
I'm interested in providing proper bait files to Picard's CollectHsMetrics tool. From the code that I examined, bcbio currently forces both the bait file and the target file to be the same (eg: the file provided to variant_regions). This PR proposes to fix the small missing link that would allow providing a proper bait file.
config:algorithm:bait_regionsentry in the datadict, which allows for providing a path to the bait file in the yaml config.reportsmethod of the PicardMetrics instance.If anything is missing, I will gladly adapt this contribution as needed (updating the documentation, adding other missing elements that I oversaw, etc.).
Thank you!