I've been looking at this all day today, and here's what I've figured out.
The picard_wrapper.py simply puts the SAM header from the input BAM file
at the top of the BED file. However, the interval file actually has
different columns of the order:
Seq Name, Start Pos (1-based), End Pos, Strand, I
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
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
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
