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 type.
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 <ross.laza...@gmail.com> 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 > <ngsbioinformat...@gmail.com> 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 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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