Hey Ryan,
thanks for reporting this issue. We must have missed this during a
transition from a single interval list file to being able to specify
multiple interval list files, for targets and baits respectively. I have a
pull request to enforce that at least one interval list for both the
targets and baits be specified (see:
https://github.com/broadinstitute/picard/pull/91).
For your use case, you may specify the same interval list for the baits as
for the targets, and the tool should run to completion. You can then
ignore metrics related to the baits. Nonetheless, I highly recommend
specifying the baits you used in your capture.
Nils
On Mon, Oct 6, 2014 at 10:24 AM, Ryan G <[email protected]> wrote:
> Hi all - I just tried running CalculateHsMetrics without specifying a
> baits file. I only specified a target and BAM file. The error I get is
> "Cannot concatenate an emply list of IntervalLists."
>
> I stepped through the code to see what was happening and in
> CollectTargetedMetrics::doWork, there is a check to see if the sequence
> dictionaries for the baits file is the same as the BAM file. Since I'm not
> specifying a baits file this, this check fails. The docs state that baits
> file is optional. Can a check be added to see if a baits file was supplied
> be added? The error is misleading in this case.
>
>
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