Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
where do I find SamToFastq.jar ? [reproducibility?]
I am from system-administrator side, and totally new in this field about bio-informatic, so excuse my weird question.
I am attempting to reproduce results of:
Nature Biotechnology 33, 1152–1158 (2015) doi:10.1038/nbt.3344
The main issue is that they do not provide the exact versions of the used tools, neither
Now, (at least) 2 years after, it is (unfortunately) almost impossible to re-launch --as-is-- their test-cases and there is some errors, just because the User-Interface of such tools have evolved (hopefully! ;-).
I do not want to re-write and/or adapt
polysolver to the current and latest versions of the tools, just re-run the published software.
Well, I have read some Release Notes, trying to identify the versions. But, at some point, it is unfruitful... and too painful!
One of there errors is about GATK, i.e.,
Error: Unable to access jar file path/to/gatk/SamToFastq.jar
Where do I find
Does it move to Picard ?
If yes, now it seems that the UI is not
java -jar path/to/picard/picard.jar <tool-name> .... Therefore, what is the last version of Picard considering the previous UI ?
Or maybe, I am not able to correctly read the documentation and I miss a point.
Thank you in advance for any advice !
All the best!