Hi Peter,

I've uploaded updated tool_dependencies.xml to the Tool Shed, hopefully it
works (I didn't bother installing Galaxy on local machine...)


On Tue, Nov 4, 2014 at 5:44 PM, Peter Cock <p.j.a.c...@googlemail.com>

> Hi all,
> I'm looking for a little advice on the pre-existing SAM/BAM filtering
> tools already in the Galaxy Tool Shed (to avoid reinventing the wheel).
> As I mentioned on another thread, I'm working on a wrapper for the
> "samtools bam2fq" command (targeting samtools 1.1 which fixed
> some bugs in this tool and added new functionality compared to
> samtools 0.1.19), see:
> https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_bam2fq
> https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_bam2fq
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_bam2fq
> One of my motivating use cases is a workflow like this:
> 1. Upload paired end FASTQ files.
> 2. Map them against a known contaminant genome giving a BAM file
> (note I need the mapper to report unmapped reads in the output).
> 3. Filter the BAM to get unmapped reads, plus reads whose partner is
> unmapped (conversely, remove reads where both partners are mapped).
> 4. Convert the filtered BAM back into FASTQ (with samtools bam2fq).
> 5. Proceed with analysis (e.g. de novo assembly).
> Assuming I have understood "samtools view", this filtering step
> has to be multiple parts:
> This would get the unmapped reads
> $ samtools view -f 0x4 ...
> This would get reads with an unmapped partner:
> $ samtools view -f 0x8 ...
> However this would only get unmapped reads with an unmapped partner:
> $ samtools view -f 0x12 ...
> i.e. samtools view allows logical AND, not logical OR, when combining
> flag filters.
> So, I believe using samtools directly, a two stage filter is needed
> followed
> by a merge (and sort), taking care not to duplicate reads, perhaps:
> $ samtools view -f 4 ... > unmapped.bam
> $ samtools view -f 8 -F 4 ... > mapped_with_partner_unmapped.bam
> $ samtools merge unmapped.bam mapped_with_partner_unmapped.bam > ...
> That could be repeated within Galaxy but is surprisingly complicated
> with multiple steps in the history - so I do not want to go that route.
> Have I overlooked a simple ToolShed solution using samtools?
> As far as I could tell, the only other option on the current Tool Shed
> is the Sambamba Filter tool (using "unmapped or mate_is_unmapped"),
> which has a very capable looking filter system:
> https://toolshed.g2.bx.psu.edu/view/lomereiter/sambamba_filter
> @Artem - have you explored updating your tool_dependencies.xml
> to download your pre-compiled binaries by default? That would
> make deployment far easier, since D compilers are still rare, and
> would mean we can see the test results on the Tool Shed :)
> Please ask if you'd like advice on Tool Shed packaging.
> Thanks,
> Peter
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