Hi all,
I have a list of more than 100 SNPs (rsXXXXXX) and I would like to obtain the different allele frequencies that each of them shows in each of the 1000Genomes populations (if possible not manually...). Is there any tool, R package etc, that allows to download them all at once? I've thought that I could maybe obtain those frequencies from the UCSC database or directly from the 1000Genomes database, but I'm open to any suggestions. Thank you very much in advanced!
Solution 1: The raw variant call data can be downloaded from http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ . Once you have those files, the INFO column in each VCF file contains superpopulation allele frequencies, and there are a bunch of tools which can look up the INFO column entry for a particular rsID. The one complication is that, since there's a separate VCF file per chromosome, you may first need to figure out which rsIDs are on which chromosomes.
Solution 2: With plink 2.0, http://www.cog-genomics.org/plink/2.0/resources#1kg_phase3 provides a single merged dataset containing all chromosomes (download the boldfaced links, then rename phase3_corrected.psam to all_phase3.psam). Then,
plink2 --pfile all_phase3 vzs --extract [your list of rsIDs] --export vcf
can then be used to export a VCF with only the rsIDs you care about; the precomputed superpopulation allele frequencies will be in the INFO column of this freshly generated VCF. You can also define your own populations with --keep and compute allele frequencies on the fly with --freq.
Sorry, I don't know what might be happening but my plink2 returns that it doesn't recognise the "--pfile" option... I'm launching the command in a folder with the files all_phase3.pgen.zst, all_phase3.psam, all_phase3.pvar.zst and my list of rsIDs... is it possible that it is not recognising some of the files? Or is it more likely a problem of my plink2 installation?
Thanks again :)
You need to decompress the .pgen.zst file first; see the instructions at the top of the resources page.
This requires plink 2.0, not 1.9. What do you get when you type “plink2 —version”?
$ cat rslist.txt | while read R ; do wget -q -O - "https://www.ncbi.nlm.nih.gov/snp/${R}?download=frequency" | grep -E '^(#Study|1000Genomes)' | sed "s/^/${R}\t/" ; done
rs25 #Study Population Group Samplesize Ref Allele Alt Allele BioProject ID BioSample ID
rs25 1000Genomes Global Study-wide 5008 T=0.485 C=0.515 PRJEB6930 SAMN07490465
rs25 1000Genomes African Sub 1322 T=0.493 C=0.507 SAMN07486022
rs25 1000Genomes East Asian Sub 1008 T=0.474 C=0.526 SAMN07486024
rs25 1000Genomes Europe Sub 1006 T=0.521 C=0.479 SAMN07488239
rs25 1000Genomes South Asian Sub 978 T=0.52 C=0.48 SAMN07486027
rs25 1000Genomes American Sub 694 T=0.38 C=0.62 SAMN07488242
rs26 #Study Population Group Samplesize Ref Allele Alt Allele BioProject ID BioSample ID
rs26 1000Genomes Global Study-wide 5008 T=0.335 C=0.665 PRJEB6930 SAMN07490465
rs26 1000Genomes African Sub 1322 T=0.404 C=0.596 SAMN07486022
rs26 1000Genomes East Asian Sub 1008 T=0.291 C=0.709 SAMN07486024
rs26 1000Genomes Europe Sub 1006 T=0.341 C=0.659 SAMN07488239
rs26 1000Genomes South Asian Sub 978 T=0.36 C=0.64 SAMN07486027
rs26 1000Genomes American Sub 694 T=0.22 C=0.78 SAMN07488242
rs27 #Study Population Group Samplesize Ref Allele Alt Allele BioProject ID BioSample ID
rs27 1000Genomes Global Study-wide 5008 G=0.283 C=0.717 PRJEB6930 SAMN07490465
rs27 1000Genomes African Sub 1322 G=0.355 C=0.645 SAMN07486022
rs27 1000Genomes East Asian Sub 1008 G=0.284 C=0.716 SAMN07486024
rs27 1000Genomes Europe Sub 1006 G=0.261 C=0.739 SAMN07488239
rs27 1000Genomes South Asian Sub 978 G=0.29 C=0.71 SAMN07486027
rs27 1000Genomes American Sub 694 G=0.16 C=0.84 SAMN07488242
rs28 #Study Population Group Samplesize Ref Allele Alt Allele BioProject ID BioSample ID
rs28 1000Genomes Global Study-wide 5008 C=0.517 T=0.483 PRJEB6930 SAMN07490465
rs28 1000Genomes African Sub 1322 C=0.601 T=0.399 SAMN07486022
rs28 1000Genomes East Asian Sub 1008 C=0.476 T=0.524 SAMN07486024
rs28 1000Genomes Europe Sub 1006 C=0.517 T=0.483 SAMN07488239
rs28 1000Genomes South Asian Sub 978 C=0.53 T=0.47 SAMN07486027
rs28 1000Genomes American Sub 694 C=0.40 T=0.60 SAMN07488242
Thank you so much for this solution @Pierre. Could you please tell me how can i write this to a file versus printing it on my screen because I need to get the frequencies for around 500 variants. Thank you so much!
how can i write this to a file versus printing it on my screen
https://www.tecmint.com/linux-io-input-output-redirection-operators/
Log in to answer this question.
http://www.internationalgenome.org/faq/can-i-find-genomic-position-list-dbsnp-rs-numbers-0/ BioMart allows to filter fo specific variant IDs.
This only provides genomic positions, not population allele frequencies.