Broken GATK4 documentation links
REQUIRED for all errors and issues:
a) GATK version used:
Many links on many documentation pages for GATK, but exemplified in the following by version 4.5.0.0 documentation
b) Exact command used:
Clicking a link
c) Entire program log:
None
Dear GATK support team,
I find it quite hard to seek out proper documentation for the various tools you so kindly provide. This is because many documentation papers link to other papers/ressources, but in many cases the links do not work. It may be a redirection problem. I used to think that links were broken because of reorganization, but I continue to experience the problem also in newer documents. For instance, on the documentation page for HaplotypeCaller there is a link to recommendations for proper input formatting. The link points to the following URL:
https://software.broadinstitute.org/gatk/documentation/article?id=4067
However, if it is clicked or if the URL is actively pasted in the browser, I am redirected to the following address:
https://gatk.broadinstitute.org/hc/en-us
The same redirection takes place for many, many links, which altogether makes it quite hard to find the appropriate information for many tools. I hope there is an explanation and a solution. Thanks in advance.
Best,
Steffen
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This has been a known issue and we are working on getting it resolved. Some of those links were remnants of the old version of the zendesk that we are using and new zendesk migration clearly changed the way those articles are indexed in an unexpected way and we are getting to update our links.
Can you point me towards the actual article that you find this link on? I will see what the problem is and fix it if it is an easy one.
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Dear Gökalp Çelik
Thank you for looking into this. The article containing the mentioned link can be found here:
https://gatk.broadinstitute.org/hc/en-us/articles/21905025322523-HaplotypeCaller
There are several links in the article having the issue, though. The specific link, I referred to is tied to the word "here", which is the last word in the final paragraph before the following headline:
How HaplotypeCaller works
After this headline, there are four numbered headlines that are also links that have the issue. Furthermore, there is a problematic link tied to the words "allele-specific annotations", a problematic link tied to the word "bamout", and finally a problematic link tied to the words "this document" in the last bullet under Additional Notes.
So for this article alone, I found eight broken links - I imagine it cannot be a small task to fix such issues throughout the site. Would it be a help to you if we, the grateful users, would continue to send you feedback when we come across such broken links? Thank you.
Best, Steffen
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Hi again. These documentation links are tied to the GATK source code directly thus compiled during the time of release. Thank you for indicating this issue here. We will update the source code with proper links and new release will sure contain proper links directly.
For the link you mentioned in the first part is related to RNAseq variant calling best practices document from a distant past but we have a newer version in the making and you can consult to that one
In summary STAR aligned reads should be processed with our tool SplitNCigarReads to be compatible with HaplotypeCaller to perform its function.
I hope this helps.
Regards.
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Thank you very much!
Regards
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