Yes, the Picard tool mandates a bizarre bait/target format file for
reasons which might best be addressed to the Picard devs - they may
have some very good reasons although I can't imagine what they are.
Yes, automated conversion of any valid Galaxy bed dataset into the
strange format required by the Picard tool is a very good idea. We're
already half way there because the tool wrapper adds the (IMHO really
silly) required SAM header automagically.
A new datatype (eg "picardBaitTarget") and an automated converter
would make the tool much easier to use - it's far from ideal to force
Galaxy users to comply with the strange Picard format requirements if
we can automate a converter.
I thought about implementing one but stopped when I realized that am
not sure what an automated converter should do if the user supplies a
valid Galaxy bed lacking strand information - generally, making up
strand is not a good idea. I don't have enough insight into the way
the stats are calculated to know whether bad things might happen if
(eg) we assume all the bait and target regions are on the + strand if
they're not - but if someone can describe how to automate the
conversion, it would definitely be an improvement to the usability of
the Picard tool.
On Tue, Jan 10, 2012 at 8:03 AM, Ryan Golhar
> Hi all - I think there is a problem with the Picard HSMetrics wrapper in
> Galaxy. The wrapper accepts a BAM files and a BED file. However the BED
> file isn't really in a BED format...it requires a SAM header before the BED
> lines. This really isn't a BED file format. I'm not quite sure how Galaxy
> should deal with this...maybe a file format specific for Picard formatted
> BED file.
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Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
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