Re: [galaxy-user] GATK - Base recalibrator

Hi Frank, Yes, that's equivalent; BaseRecalibrator is a single tool that combines those two steps in more recent versions. The version of GATK in Galaxy (1.6 afaik) is a pretty old one. I would strongly recommend using the most recent version of GATK (2.8) as it will give you better results. Good

[galaxy-user] GATK - Base recalibrator

Hi all, I'm trying to call variants using GATK best practices workflow. So after performing Realigner Target Creator step, one should jump on Base Recalibrator step. Unfortunatly, I don't see this program under GATK tab. Is there a way to perform this step in Galaxy? There are the Count covari

[galaxy-user] GATK error Argument with name 'T' isn't defined

Aloha. I am using GATK in Galaxy for the first time, on a local Galaxy server, and when I try to run Count Covariates I get the error: ERROR stack trace org.broadinstitute.sting.commandline.InvalidArgumentException: Argument with name 'T' isn't defined. at org.broadinstitute.s I have looked at

Re: [galaxy-user] GATK Not running

: total time 0.06 From: Daniel Blankenberg [d...@bx.psu.edu] Sent: Wednesday, December 12, 2012 4:29 PM To: Farooq,Umar (res) Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] GATK Not running Hi Umar, Can you click the eye icon to view the contents

Re: [galaxy-user] GATK Not running

Hi Joshua, Is this on the main public site? If so, can you share your history with me and I'll take a look? If this is on a local instance, can you provide additional information, such as the GATK version that you are using? Thanks for using Galaxy, Dan On Dec 11, 2012, at 5:34 PM, Joshua Or

Re: [galaxy-user] GATK Not running

Hi Philippe, The GATK wrappers provided with the Galaxy distribution are for GATK version 1.4. There is a set of 1.6/GATK-lite wrappers that has been developed by the team, but is not yet available. There may also be other options available in the Tool Shed that have been contributed by the com

Re: [galaxy-user] GATK Not running

Hi Umar, Can you click the eye icon to view the contents of the 'log' dataset for the GATK run. The end of the log should have the actual error encountered (the text you provided is a bit of a red herring) Since you are using hg19, the most likely cause for the error is that the reference fast

Re: [galaxy-user] GATK Not running

ssentially cannot use GATK in galaxy. From: Joshua Orvis [jor...@gmail.com] Sent: Tuesday, December 11, 2012 5:34 PM To: Philipe Moncuquet Cc: Farooq,Umar (res); galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] GATK Not running I'm having som

Re: [galaxy-user] GATK Not running

I'm having some problems with GATK as well, but do have a functional pipeline that uses the following GATK tools in Galaxy: - Realigner Target Creator - Indel Realigner - Unified Genotyper - Variant Filtration The main problem I'm having with them is that it seems I need to run the fasta/fastq gr

Re: [galaxy-user] GATK Not running

Hi, I have encountered the same kind of errors. When I update the loc files link to GATK, some of the tools display the reference genomes I added and some not. It seems that the galaxy wrapper for GATK 1.6 is not very functional. GATK don't really care because they are not supporting it any more,

[galaxy-user] GATK Not running

Hi, I am trying to incorporate GATK in my pipeline but not been able to make it work. I aligned my data with Hg 19 and then ran sam tool filter and then picard duplicate removal. I uploaded dbSNP and the reference FASTA file for Hg 19 in galaxy to run this pipeline. But for some reason GATK too

[galaxy-user] GATK workshop survey

For Galaxy users who use the GATK tools: The GATK team at the Broad Institute is planning a workshop for users this Fall. If you're interested in attending the workshop, you can vote on the topics and activities that you'd like the workshop to include by filling in this survey: GATK workshop surve

Re: [galaxy-user] GATK tools: other genome available?

Hello Jean, There is no method for transferring existing genomes/indexes to user histories. This tool set is brand-new on the public server and is released as beta. In the near-term, more genomes will be indexed and added, but for now, using a Custom reference genomes is the available option

[galaxy-user] GATK tools: other genome available?

Hi, The NGS: GATK Tools on main are so far only for human genome. Do you have an idea when other genomes (such as my favorite, i.e mice and mm9) would be accessible ? Otherwise, is there a way to easily transfer "mm9 genome that is system-installed on main" directly in a "Custom build genome" t

Re: [galaxy-user] GATK wrapper in Galaxy

Hi Mike, Apologies for the delay in reply, your message was threaded under an announcement (perhaps accidentally sent as a reply to that thread?). For GATK, we are not offering support yet as the pipeline is still considered beta. Most tool that are only on Test, and not on Main, are conside

Re: [galaxy-user] GATK

Hi Franzi, You have one too many hg19 in there. The fields go like: so: hg19hg19hg19 /drive1/galaxy/reference/hg19/sam_index/hg19_ref.fa gatk But do note that these tool integrations are still undergoing active development. Please report bugs if you encounter a

Re: [galaxy-user] GATK

Hi Metge, Thank you for your kind comments! The GATK tool wrappers are still in an early beta stage of development. Because of this, we are not ready to support set-up in local instances yet. If you have functionality input for the version on our Test server, general feedback is welcomed on

[galaxy-user] GATK

Dear happy users of Galaxy, We are running Galaxy locally. It's a very fine tool! By now everything works fine, except when I try to run any GATK program. I usually get this error message: # ERROR --

[galaxy-user] GATK wrapper in Galaxy

Hello all,   I am trying to run through the GATK pipeline on the Galaxy Test page. I have a question related to the UnifiedGenotyper wrapper page. At the bottom of the page, I choose the "Advanced" tab for "Basic or Advanced Analysis options."    After the automatically refreshed, I choose the "

Re: [galaxy-user] GATK

Hi Danny, On 10/28/11 8:53 AM, Muehlschlegel, Jochen D.,M.D. wrote: Hi Jen, Great. I am uploading data right now and will try it. It would be a great addition if it worked and I will give you feedback. On another note, is Galaxy in the meantime able to do a cufflinks, specifically Cuffdiff ana

Re: [galaxy-user] GATK

Hi Danny, A beta GATK pipeline is available on our Test instance at: http://test.g2.bx.psu.edu/ Feedback about the tool suite is welcomed! Best, Jen Galaxy team On 10/27/11 1:08 PM, Muehlschlegel, Jochen D.,M.D. wrote: Hi, Do you host GATK on the Galaxy server? If not, is there a way to c

[galaxy-user] GATK

Hi, Do you host GATK on the Galaxy server? If not, is there a way to call SNPs from NGS (RNA-seq) data using Galaxy ? Thanks Danny The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contai

Re: [galaxy-user] GATK best practices with local installation of Galaxy

Hi, Camille. If you can find some time to upload some of your bam files, could you please test the revised bam merge tool on http://test.g2.bx.psu.edu/ and let me know how you go. This won't be on the main site until the next scheduled update in a few weeks. If you need this locally, the changes

Re: [galaxy-user] GATK best practices with local installation of Galaxy

Hi, Camille, I can see this really needs a 'proper' fix - preferably taking advantage of the automated header merge. Preserving the metadata from each bam automatically is safer and less error-prone but you could use the existing "Replace sam/bam header" tool to do the surgery once you have a corr

Re: [galaxy-user] GATK best practices with local installation of Galaxy

Hi Ross, thanks for your answer. I found a dirty fix for merging pairs of bam files, had to change a couple of things in my local installation though. - Add group reads to each BAM file separately using Picard's Add or Replace Groups (with ID

Re: [galaxy-user] GATK best practices with local installation of Galaxy

Camille, thanks for reporting this - I think you have found a bug. We definitely need to be able to preserve metadata when we merge bams. Thanks for your suggestion of using mergeSamFiles - yes, I think it might be a good fix for this problem - but it will take a little while and won't reach the Ma

[galaxy-user] GATK best practices in local installation of Galaxy

Hello guys, I'm trying to run a pipeline of the best practices for snp and indel discovery as described by the people at Broad and I'm running into troubles with the GATK tools in a local installation of Galaxy. The main problem I have is that merging bam files with the samtools merge tool doesn't

[galaxy-user] GATK best practices with local installation of Galaxy

Hello guys, I'm trying to run a pipeline of the best practices for snp and indel discovery as described by the people at Broad and I'm running into troubles with the GATK tools in a local installation of Galaxy. The main problem I have is that merging bam files with the samtools merge tool doesn't