Hi Claire,
Your welcome!.
If you feel it could be helpful, this is what I have so far as a
workflow for GATK:
http://test.g2.bx.psu.edu/u/cjav/w/gatk
Is not complete, but I think it could be a good starting point. Please
if you ended using this workflow as a starting point and find
something you
Hi Carlos,
Thanks! I didn't realise the conversion was doing that.
In fact I want bam files (I'm also using GATK) so this is really helpful.
Cheers,
Clare
On Thu, Jan 19, 2012 at 2:32 AM, Carlos Borroto
wrote:
> Hi Clare,
>
> I ran into a similar question testing out GATK pipeline on Galaxy. M
Hi Clare,
I ran into a similar question testing out GATK pipeline on Galaxy. My
solution was to always convert my SAM files to BAM. The wrapper also
sorts the final BAM file output and it does this using the known
'samtools sort', which sorts chromosomes in the same order of the
reference genome.
Hi Jen,
Thanks for this, belatedly! And happy new year!
I think this will work for some of my cases but possibly not all,
since it looks like chromosomes are being sorted alphabetically. It
depends what the reference genome used was and what tools you're
planning to use after sorting as to wheth
Hello Clare,
An example of how to sort a SAM file is included in the workflow from #2
on this FAQ (it can be imported and the sort modified as needed):
http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq
If you are starting with a BAM file, convert BAM->SAM, then after
sorting, back wi
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