Trying to find file tutorial_8017 for GATK tutorial from the Broad Institute

Question

[appropiate]

I wanted to follow the tutorial named "Map reads to a reference with alternate contigs like GRCH38" from https://gatk.broadinstitute.org/, which refers to a currently inactive ftp link to download the file tutorial_8017.tar.gz contatining the test data needed to follow along the tutorial. I have also tried to look on their google buckets

gatk-test-data

broad-public-datasets

mentioned in another document, but the file does not seem to be there either. Any idea of its availability elsewhere?

[Ram]

Your previous post was marked as spam by the spambot owing to URLs in the title. I've removed it from spam and deleted it as a duplicate. Sorry about the inconvenience caused by the spambot!

[appropiate]

Thanks! I was trying to delete it myself, how could I do that? I do not see the "moderate" button to delete my posts, which I read about in another post.

[Ram]

Maybe your browser has JavaScript disabled? It should be right next to the edit button:

[appropiate]

Next to the edit button I have a "Following with messages" dropdown menu that does not include delete option. I tried Chrome and Firefox in Ubuntu 20.04, but I do not see the moderate button. I read that both Chrome and Firefox no longer have NPAPI support (technology required for Java applets), so if this is the reason, which browser should i use instead?

[appropiate]

Sorry I misread, and thought you meant Java. In Chrome settings it shows that sites can use Javascript.

[Ram]

Can you show me a screenshot of your top level post so the entire post is covered like so:

[appropiate]

[Ram]

I'm not sure why you don't have moderate privileges on your own posts - maybe one of the site admins can comment on this. I'll alert them to this post.

[Ram]

Turns out that the moderate button is available to moderators only. This change came into effect when the website upgraded to a new version a few months ago.

To delete your post, click on Edit and look for the Delete button on the right just below the post preview.

[appropiate]

Oh yes, I see the delete button when editing, thanks a lot @Ram!!

Answer 1

[GenoMax]

This should get you the data you need:

$ wget -O tutorial_8017.tar.gz ftp://[e-mail]/tutorials/datasets/tutorial_8017.tar.gz

[appropiate]

Great, thanks!

[appropiate]

Sorry to bother you again @GenoMax, do you happen to know how the chr19_chr19_KI270866v1_alt.fasta.alt index file included in tutorial_8017.tar.gz was generated? I do not find clear information on this, but it doesnt look like bwa index does it.