In case anyone is interested I posted a message to samtools-dev and got a
few responses about it.  The thread is called 'Picard bait/target format
file for HsMetrics'.  Now, for Galaxy, I think the wrapper should not
accept the BED file as input as that doesn't work.  I like the idea of a
new file format (picardBaitTarget or maybe picardIntervalList) as the input

If the converter tool adds a header to the BED file, then there is the
possibility that a user can associated the BED file with the wrong version
of a genome.  This is what Picard was trying to avoid.  But that doesn't
mean a user can't manually add the wrong header anyway.  If the BED file is
missing strand information, I don't think the tool should add it.  I would
say just leave the rest of the file alone.  If there is no strand
information, perhaps the user doesn't care about the strand.

On Mon, Jan 9, 2012 at 6:11 PM, Ross <> wrote:

> Hi Ryan,
> 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.
> Suggestions welcomed!
> On Tue, Jan 10, 2012 at 8:03 AM, Ryan Golhar
> <> wrote:
> > 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 requires a SAM header before the
> > 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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