# Having issue with exome sequencing - Deprecated tool (BWA for Illumina) in older workflow

**URL:** <https://help.galaxyproject.org/t/having-issue-with-exome-sequencing-deprecated-tool-bwa-for-illumina-in-older-workflow/592>\
**Category:** Uncategorized\
**Tags:** bwa-for-illumina, bwa, bwa-mem, tool-deprecated\
**Created:** [February 10, 2019, 7:51pm UTC](https://help.galaxyproject.org/t/having-issue-with-exome-sequencing-deprecated-tool-bwa-for-illumina-in-older-workflow/592 "2019-02-10T19:51:55Z")\
**Posts on this page:** 1\
**Showing post:** 2

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**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:** [February 11, 2019, 1:16am UTC](https://help.galaxyproject.org/t/having-issue-with-exome-sequencing-deprecated-tool-bwa-for-illumina-in-older-workflow/592/2 "2019-02-11T01:16:07Z")

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> [@Mo123](#):
>
> [Galaxy](https://usegalaxy.org/u/jeremy/w/exome-analysis)

Hi - This workflow is over 5 years old (from 2014) and most of the tools included now have newer versions and should be updated in the workflow before use. In particular, the `BWA for Illumia` tool has been deprecated and can produce unexpected results/errors. It seems like you are not getting any hits.

Either `BWA` or `BWA-MEM` are a better choices for mapping. If you do not get hits again, you’ll need to check your inputs and tool settings.

FAQs: [Galaxy Support - Galaxy Community Hub](https://galaxyproject.org/support/#troubleshooting)

The Galaxy tutorials include updated tools/methods/workflows. You will probably want to review those in the category _Variant Analysis_.

> [@Troubleshooting resources for errors or unexpected results](https://help.galaxyproject.org/t/troubleshooting-resources-for-errors-or-unexpected-results/42/1):
>
> [Galaxy Training Network Tutorials](https://galaxyproject.github.io/training-material/): Some [GTN](https://galaxyproject.org/teach/gtn/) tutorials are appropriate for [Galaxy Main](https://usegalaxy.org) and some are not. Where you can run each is noted per tutorial – click on the _Galaxy instances_ gear icon ![galaxyserversGTN](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/1X/1287f50cfcdaa1aad750fe323f96995260ac4947.png) to review the [Public Galaxy](https://galaxyproject.org/use/) server choices. If a tutorial is supported by a pre-configured [Galaxy Docker](https://hub.docker.com/r/bgruening/galaxy-stable/) training image, instructions for how to get it will be listed below the tutorial listings, per category.

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_[View the full topic](https://help.galaxyproject.org/t/having-issue-with-exome-sequencing-deprecated-tool-bwa-for-illumina-in-older-workflow/592)._