Questions tagged [1000genomes]

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Removing common variants in the 1000 genomes database from .vcf [closed]

I have 15 .vcf files. I need to remove `common variants in the 1000 genomes database' appearing in at least 0.5% of the population Do you know from where I may start? Thank you so much
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Obtaining HGDP project data in fasta format

I need to obtain sample data from modern humans in fasta format. I just need some megabytes of data from every individual. I actually use a script that obtains the cram file from here (ftp.1000genomes....
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1answer
50 views

There's a faster way to download 1000 Genomes phase 3?

I'm trying to download the 1000 Genomes (phase 3) through FTP, but it's taking ages. I saw the documentation about using Aspera (fasp protocol), but the instructions don't work: ...
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1answer
67 views

Simulating phenotype with the 1000 Genomes Project

I'm looking for a way to simulate phenotypes against a real SNP data source, such as the 1000 Genomes. It must be free for commercial purpose (Eg.: MIT license). Any recommendation? I'm trying to use ...
1
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2answers
60 views

1000 genomes missing SNPs on chr X in GRCh38

I am trying to get a reference together for imputation using the 1000 genomes data set. The GRCh38 version of the data set was made available earlier this year, but seems to be missing a significant ...
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1answer
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what is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets?

What is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets nowadays? About 5 years or so ago, it used to be the latest release of the CSHL ...