1000 Genomes phase 3 filename extension

[Fedik Rahimov]

Hello Chris,

I downloaded some "1000 Genomes phase 3" files from https://www.cog-genomics.org/plink/2.0/resources#phase3_1kg.

Both pgen and pvar files end with "?dl=1", which I guess I have to remove in order to use these files. In that page you also note  Remove "_rs" from the .pvar.zst filenames before use. But I do not see any "_rs" in pvar filenames. What do you mean by removing "_rs"?

Thank you

[Christopher Chang]

How are you downloading these files?  What checkboxes did you select/unselect, and what's the full filename of one of these .pvar.zst files you're asking about?

[Fedik Rahimov]

I downloaded  these three files with wget on a linux HPC, also on a Mac using wget on terminal

https://www.dropbox.com/s/j6cuuc8q1jzwj9y/chr16_phase3.pgen.zst?dl=1

https://www.dropbox.com/s/5ynstl55kcahpmr/chr16_phase3.pvar.zst?dl=1
https://www.dropbox.com/s/6ppo144ikdzery5/phase3_corrected.psam?dl=1

the downloaded pvar file name appears like this chr16_phase3.pvar.zst?dl=1

Checked boxes were: Split by chromosome, INFO annotations, and KING-based pedigree corrections

[Chris Chang]

When that set of checkboxes is selected, “Remove ‘_rs’” should not be displayed on the webpage.  The webpage text changes when you toggle the checkboxes.

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[Fedik Rahimov]

Now I see that the 2022-08-04 Byrska-Bishop et al callset pvar filenames have an "_rs" in the file name , not other callsets. Maybe this note can be hidden for the other two callsets.

[Fedik Rahimov]

I am not sure if you mean these three checkboxes, but it is displayed. Please see the screenshot.

[Christopher Chang]

Yes, I see the issue now, thanks for clarifying.  That sentence should be removed now under this callset/checkbox combination.