Brad Chapman

Scott; I've been fruitlessly trying to dig for an error in this file and haven't been able to find anything yet after running through a few different validation tools. So...

Scott; I don't think that step is essential, unless your reference genome has non-N ambiguous bases, so you could skip it. If you want to include it, it's only a...

Seamus; Thanks for trying this out and sorry about the issues. Right now it doesn't handle gVCF files, which contain data for non-variant regions (labelled with the `NON_REF` variant). Generally...

Piet; Thanks for trying out bcbio.variation and for the very complete report. It looks like something is unexpected with your bed file `ref.bed`. Specifically, do the start/end coordinates in the...

Piet; Would you be able to provide your BED file input as a Gist (https://gist.github.com/) or send to me directly? Maybe we'll be able to figure out the underlying issue...

Piet; bcbio doesn't have any special requirements for headers or columns. Where it is failing it is only trying to split the line by tabs and then take the first...

Piet; Thanks much for following up and for the details about the line endings. I pushed a fix which should handle this for future files by stripping off stray whitespace....

Sakina; Thanks for the report. Happy to look at this if you could make the log and validation files available at a Gist (https://gist.github.com/). Thanks much.

Sakina; Thanks for the additional detail. It appears as if something is wrong with one of your input VCF files, specifically that is has truncated lines. The code is failing...

Sakina; Thanks for looking into this more. I added better debugging into a snapshot release of bcbio.variation. If you could download this and replace the existing version this should hopefully...