Lisle Mose

Thanks, this looks perfect for validating against a somatic truth set. However, if I wanted to run against the Genome In a Bottle Truth set, I'm not sure this would...

One such use case where leniency is desired is calling variants against RNA and validating against a truth set generated from DNA. In this case, we don't know ground truth...

We currently skip header lines starting with what I understand to be the standard bed header text. i.e. browser, track or # Let me know if you are seeing otherwise.

I'm not sure I have a grasp on the issue here. Based on a quick reading of the SAM spec, I could not anything to support the following statement: >...

Also, it may be helpful to hear how this is impacting downstream tools your are using with the realigned BAM. Thanks.

Thanks for reporting this. Are you looking for the realigned reads to also use the = X format?

Thanks for reporting this. At present, supplementary alignments are eligible for realignment just like other reads - and this may not be the best behavior. The removal of hard clips...

There is an issue with commas being used as the decimal place with your locale. I will address this in the software in a future release. As a workaround, please...

Unless you have a specific reason to compile, try using one of the precompiled releases. Otherwise, you'll need to configure your system to have the C standard library files available...

Ah, yes. The precompiled versions will not work on Mac. A quick Google search suggests to install xcode. I have not attempted to run on Mac myself.