# Exome sequencing data analysis for diagnosing a genetic disease: Problem in Finding and reporting plausible causative variants step **URL:** \ **Category:** usegalaxy.org support\ **Tags:** gtn-tutorial, variant-analysis\ **Created:** [September 2, 2024, 9:59am UTC](https://help.galaxyproject.org/t/exome-sequencing-data-analysis-for-diagnosing-a-genetic-disease-problem-in-finding-and-reporting-plausible-causative-variants-step/13360 "2024-09-02T09:59:51Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![Adhichoz08](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/adhichoz08/32/6019_2.png) [@Adhichoz08](https://help.galaxyproject.org/u/Adhichoz08)\ **Post date:** [September 2, 2024, 9:59am UTC](https://help.galaxyproject.org/t/exome-sequencing-data-analysis-for-diagnosing-a-genetic-disease-problem-in-finding-and-reporting-plausible-causative-variants-step/13360/1 "2024-09-02T09:59:51Z")
Hi, I am Athithyan Chozhan from India I tried to replicate the tutorial : Exome sequencing data analysis for diagnosing a genetic disease and in the final step: Finding and reporting plausible causative variants step I did not got any variants corresponding to the phenotype Please have a look and guide me ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/7/7e46c150b22cd6bbf9793da4020e1bcb7830e684.png) ---
**Author:** ![Adhichoz08](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/adhichoz08/32/6019_2.png) [@Adhichoz08](https://help.galaxyproject.org/u/Adhichoz08)\ **Post date:** [September 2, 2024, 10:00am UTC](https://help.galaxyproject.org/t/exome-sequencing-data-analysis-for-diagnosing-a-genetic-disease-problem-in-finding-and-reporting-plausible-causative-variants-step/13360/2 "2024-09-02T10:00:51Z")
> **[Galaxy](https://usegalaxy.org/datasets/f9cad7b01a47213545bab2a5717d71c3/preview)** > > Galaxy is a community-driven web-based analysis platform for life science research. ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [September 3, 2024, 8:43pm UTC](https://help.galaxyproject.org/t/exome-sequencing-data-analysis-for-diagnosing-a-genetic-disease-problem-in-finding-and-reporting-plausible-causative-variants-step/13360/3 "2024-09-03T20:43:51Z")
Welcome, @Adhichoz08 The link you shared is a link to an empty job details page. Very odd! Would you please share your history instead? That will make it much more likely that we can isolate what is going wrong and offer advice. See the banner at this forum, or here directly for how to do this → [How to get faster help with your question](https://help.galaxyproject.org/docs?topic=11469) And, there is another strategy: since you already have the starting data in your history, you can _also_ load up the tutorial’s workflow, then run the workflow. Check the box to send the workflow output to a new history. You can then use that new history as a sort of “answer key” to compare the manual steps to. Maybe do both, and post all the links back? And we can follow up with the details with that context. Thanks! 🙂 ---
**Author:** ![Adhichoz08](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/adhichoz08/32/6019_2.png) [@Adhichoz08](https://help.galaxyproject.org/u/Adhichoz08)\ **Post date:** [September 4, 2024, 5:45am UTC](https://help.galaxyproject.org/t/exome-sequencing-data-analysis-for-diagnosing-a-genetic-disease-problem-in-finding-and-reporting-plausible-causative-variants-step/13360/4 "2024-09-04T05:45:08Z")
Thank you very much for your kind response Here I am attaching the history link for your reference > **[Galaxy](https://usegalaxy.org/published/history?id=a4a2fcda44fc0241)** > > Galaxy is a community-driven web-based analysis platform for life science research. As you said , I am running the tutorial workflow currently and it is going well so far I will reply to this post once finished Please refer the history link ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [September 4, 2024, 7:52pm UTC](https://help.galaxyproject.org/t/exome-sequencing-data-analysis-for-diagnosing-a-genetic-disease-problem-in-finding-and-reporting-plausible-causative-variants-step/13360/5 "2024-09-04T19:52:24Z")
Hi @Adhichoz08 I was able to run the tutorial data and workflow (from the tutorial, not from someone else) as well, and am posting back the completed history. shared here → [https://usegalaxy.org/u/jen-galaxyproject/h/exome-seq-training-full-w-cached-ref](https://usegalaxy.org/u/jen-galaxyproject/h/exome-seq-training-full-w-cached-ref) I’m looking at your history next, but let me know if you solve this before I am able to do that and reply, thanks! 🙂 ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [September 4, 2024, 8:04pm UTC](https://help.galaxyproject.org/t/exome-sequencing-data-analysis-for-diagnosing-a-genetic-disease-problem-in-finding-and-reporting-plausible-causative-variants-step/13360/6 "2024-09-04T20:04:02Z")
Update It looks like the first round through worked Ok, then the next cycle through had a problem with the FreeBayes run. There is not an obvious reason for that failure (empty result), maybe there was just some cluster hiccup. That means a rerun might be enough. I started that rerun up in my copy of your history here → [https://usegalaxy.org/u/jen-galaxyproject/h/copy-of-whole-exome-sequencing-learning-httpshelpgalaxyprojectorgtexome-sequencing-data-analysis-for-diagnosing-a-genetic-disease-problem-in-finding-and-reporting-plausible-causative-variants-step133603](https://usegalaxy.org/u/jen-galaxyproject/h/copy-of-whole-exome-sequencing-learning-httpshelpgalaxyprojectorgtexome-sequencing-data-analysis-for-diagnosing-a-genetic-disease-problem-in-finding-and-reporting-plausible-causative-variants-step133603) ---
**Author:** ![Adhichoz08](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/adhichoz08/32/6019_2.png) [@Adhichoz08](https://help.galaxyproject.org/u/Adhichoz08)\ **Post date:** [September 5, 2024, 1:36pm UTC](https://help.galaxyproject.org/t/exome-sequencing-data-analysis-for-diagnosing-a-genetic-disease-problem-in-finding-and-reporting-plausible-causative-variants-step/13360/7 "2024-09-05T13:36:48Z")
Dear Jenna, Thank you for your kind response and guidance. I have executed re-run Freebayes data to the following steps and at the end it provides the same result as i received before In the tutorial , it was mentioned that it is likely to find the candidate variant responsible for the phenotype. mentioned here " It was not hard to find the most likely causative mutation for the child’s disease (you did find it, right?). Even though it will not always provide as strong support for just one specific causative variant, analysis of whole-exome sequencing data of family trios (or other related samples) can often narrow down the search for the cause of a genetic disease to just a very small, manageable set of candidate variants, the relevance of which can then be addressed through standard methods." But after running GEMINI , I am getting " 0 Zero variants " Currently there is a scheduled maintanance happening , I will attach the history after clearing ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [September 5, 2024, 6:54pm UTC](https://help.galaxyproject.org/t/exome-sequencing-data-analysis-for-diagnosing-a-genetic-disease-problem-in-finding-and-reporting-plausible-causative-variants-step/13360/8 "2024-09-05T18:54:08Z")
My job in your working history completed, and it was successful. That was an exact [rerun](https://training.galaxyproject.org/training-material/faqs/galaxy/datasets_icons.html) without any changes. And, I’ve confirmed that both ran on the same cluster, so this doesn’t appear to be a larger technical issue. My best guess is that this was some transient issue, potentially just a single bad cluster node. ~~Trying again after the service event completes is a great idea~~ , or you can try now to see what happens (rerunning jobs _should_ be Ok). Looks like that completed! Thanks and let us know how this turns out! 🙂