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Update README.md
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wheaton5 authored Aug 8, 2024
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Expand Up @@ -93,11 +93,11 @@ If you have a common snps file you may want to use the --common_variants option

Common variant files from 1k genomes filtered to variants >= 2% allele frequency in the population and limited to SNPs can be found here for GRCh38
```
wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=13aebUpEKrtjliyT9rYzRijtkNJVUk5F_' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=13aebUpEKrtjliyT9rYzRijtkNJVUk5F_" -O common_variants_grch38.vcf && rm -rf /tmp/cookies.txt
curl ftp://ftp.eng.auburn.edu/pub/whh0027/common_variants_grch38.vcf.gz -o common_variants_grch38.vcf.gz
```
or for hg19 here
```
wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1lw4T6d7uXsm9dt39ZtEwpuB2VTY3wK1y' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=1lw4T6d7uXsm9dt39ZtEwpuB2VTY3wK1y" -O common_variants_hg19.vcf && rm -rf /tmp/cookies.txt
curl ftp://ftp.eng.auburn.edu/pub/whh0027/filtered_2p_1kgenomes_hg19.vcf.gz -o common_variants_hg19.vcf.gz
```

## Practice/Testing data set: Demuxlet paper data
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