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Update dropbox link and add note to 1000 Genomes vignette
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HannahVMeyer committed Aug 24, 2020
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8 changes: 7 additions & 1 deletion vignettes/Genomes1000.Rmd
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Expand Up @@ -74,11 +74,17 @@ NB: CGRCh38 positions in vcf format can be found [here](http://ftp.1000genomes.e
The remainder of this vignette will however look at the data processing required
for the 1000GenomesIII available in
[PLINK 2 binary format](https://www.cog-genomics.org/plink/2.0/input#pgen).

NB: the links to the files below are the three boldfaced links on this page:
https://www.cog-genomics.org/plink/2.0/resources#1kg_phase3. The dropbox links
have been updated in the past, which means the links below where outdated.
Please refer to the original site and open an issue on github if you notice
a change. Thank you!
```{bash download, eval=FALSE}
cd $refdir
pgen=https://www.dropbox.com/s/afvvf1e15gqzsqo/all_phase3.pgen.zst?dl=1
pvar=https://www.dropbox.com/s/0nz9ey756xfocjm/all_phase3.pvar.zst?dl=1
pvar=https://www.dropbox.com/s/op9osq6luy3pjg8/all_phase3.pvar.zst?dl=1
sample=https://www.dropbox.com/s/yozrzsdrwqej63q/phase3_corrected.psam?dl=1
wget $pgen
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