Genomic Interval File For Gatk

Question: Genomic Interval File For Gatk

7.0 years ago by

All, I'm using a locally installed galaxy with GATK 1.3 beta (recently updated). I would be interested in variant calling using GATK on both Illumina and SOLiD data. My questions are: 1) What should be the format that "Genomic Interval" option can accept in beta version. It produced an error when I provided an (enrichment coords) bed file? DepthOfCoverage had also produced error when I used bed files. Would beta release (v1.3) accept bed file as input for genomic intervals? 2) SAMtool index is seem to be missing in Galaxy. Is this true or any other module (say SAM->BAM) incorporates this functionality? Looking forward to your comments. Raj ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD

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modified 7.0 years ago by Carlos Borroto • 390 • written 7.0 years ago by Praveen Raj Somarajan • 100

7.0 years ago by

Carlos Borroto • 390

Washington Metropolitan Area

Carlos Borroto • 390 wrote:

Hi Raj, I've been also testing GATK Beta pipeline on Galaxy. This is the workflow I have so far: http://test.g2.bx.psu.edu/u/cjav/w/gatk There are a few error coming up that I haven't had the time to fix or work around yet, but I think it could be a good starting point. For example an issue with annotations in Variant Recalibrator tool, was recently fixed: https://bitbucket.org/galaxy/galaxy-central/issue/682/variant- recalibrator-error-with I haven't yet used the new manual method to enter annotations in the workflow. Regarding your questions, I don't have one for 1), I would love to hear about a solution. In my case I'm working with RNA-seq data, so I think everything would speed up if I use a good interval file, but is not clear for me at the moment how to use it or when. For 2), every time a tool outputs a BAM file in Galaxy, it is sorted and indexed automatically, in fact even if the downstream tool can use a SAM file, I still convert it to BAM just to make sure it is sorted and indexed. Regards, Carlos On Thu, Dec 8, 2011 at 1:11 AM, Praveen Raj Somarajan <

ADD COMMENT • link written 7.0 years ago by Carlos Borroto • 390

Thanks Carlos. For Q#1, I found something that GATK v1.3 does not explicity check the format of -L input file, hence the error. And the work around for commandline is to specify the format with -L, as shown below: -L:bed <interval_coords.bed> Any idea how to edit the wrapper code to resolve this issue in Galaxy? Has anybody experienced/resolved this before? Thanks, Raj. To: Praveen Raj Somarajan Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Genomic interval file for GATK Hi Raj, I've been also testing GATK Beta pipeline on Galaxy. This is the workflow I have so far: http://test.g2.bx.psu.edu/u/cjav/w/gatk There are a few error coming up that I haven't had the time to fix or work around yet, but I think it could be a good starting point. For example an issue with annotations in Variant Recalibrator tool, was recently fixed: https://bitbucket.org/galaxy/galaxy-central/issue/682/variant- recalibrator-error-with I haven't yet used the new manual method to enter annotations in the workflow. Regarding your questions, I don't have one for 1), I would love to hear about a solution. In my case I'm working with RNA-seq data, so I think everything would speed up if I use a good interval file, but is not clear for me at the moment how to use it or when. For 2), every time a tool outputs a BAM file in Galaxy, it is sorted and indexed automatically, in fact even if the downstream tool can use a SAM file, I still convert it to BAM just to make sure it is sorted and indexed. Regards, Carlos All, I'm using a locally installed galaxy with GATK 1.3 beta (recently updated). I would be interested in variant calling using GATK on both Illumina and SOLiD data. My questions are: 1) What should be the format that "Genomic Interval" option can accept in beta version. It produced an error when I provided an (enrichment coords) bed file? DepthOfCoverage had also produced error when I used bed files. Would beta release (v1.3) accept bed file as input for genomic intervals? 2) SAMtool index is seem to be missing in Galaxy. Is this true or any other module (say SAM->BAM) incorporates this functionality? Looking forward to your comments. Raj ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org<http: usegalaxy.org="">. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD

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