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cellSNP_testdata_10x.zip (129.7 MB)
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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| README.md | 2021-02-10 | 1.6 kB | |
| genome1K.phase3.SNP_AF5e2.chr1toX.hg19.vcf.gz | 2019-08-28 | 92.5 MB | |
| genome1K.phase3.SNP_AF5e2.chr1toX.hg38.vcf.gz | 2019-07-03 | 92.4 MB | |
| genome1K.subset.hg19.vcf.gz | 2019-05-21 | 153.5 kB | |
| genome1K.phase3.SNP_AF5e4.chr1toX.hg19.vcf.gz | 2018-12-21 | 453.3 MB | |
| genome1K.phase3.SNP_AF5e4.chr1toX.hg38.vcf.gz | 2018-12-06 | 568.4 MB | |
| Totals: 6 Items | 1.2 GB | 37 | |
List of common variants
This folder stores processed lists of common variants for using the package cellSNP-lite (recommended) and cellSNP.
Human variants from 1000 genome project
-
7.4M SNPs with minor allele frequency (MAF) > 0.05:
- hg19: genome1K.phase3.SNP_AF5e2.chr1toX.hg19.vcf.gz (http://ufpr.dl.sourceforge.net/project/cellsnp/SNPlist/genome1K.phase3.SNP_AF5e2.chr1toX.hg19.vcf.gz)
- hg38: genome1K.phase3.SNP_AF5e2.chr1toX.hg38.vcf.gz (http://ufpr.dl.sourceforge.net/project/cellsnp/SNPlist/genome1K.phase3.SNP_AF5e2.chr1toX.hg38.vcf.gz)
-
36.6M SNPs with minor allele frequency (MAF) > 0.0005:
- hg19: genome1K.phase3.SNP_AF5e4.chr1toX.hg19.vcf.gz (http://ufpr.dl.sourceforge.net/project/cellsnp/SNPlist/genome1K.phase3.SNP_AF5e4.chr1toX.hg19.vcf.gz)
- hg38: genome1K.phase3.SNP_AF5e4.chr1toX.hg38.vcf.gz (http://ufpr.dl.sourceforge.net/project/cellsnp/SNPlist/genome1K.phase3.SNP_AF5e4.chr1toX.hg38.vcf.gz)
All these files are based on 1000 genome project,
and processed by
this script,
which only keeps SNPs on chromosome 1 to 22 and X.
The original data is based on hg19 build, while we lifted it over to hg38 by a
Python wrap on
UCSC liftOver.