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How can I retrieve only SNPs from the dbSNP's FTP site. The files are gzipped and organized by human chromosome (i.e, chr[1-22,X,Y]), are these for one human? I need only SNPs data for various humans.

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  • $\begingroup$ Welcome to Bioinformatics. Could you please explain to which files are you talking (provide a link or explain the route to them)? I went to the ftp site and I couldn't find the folders. Related: have you look at this alert? $\endgroup$
    – llrs
    Jan 18 '18 at 8:08
  • $\begingroup$ The files present at this link ftp.ncbi.nlm.nih.gov/snp/.redesign/latest_release/JSON $\endgroup$
    – user2210
    Jan 18 '18 at 14:45
  • $\begingroup$ The readme says these files are for build 150 and the database is already by build 151 $\endgroup$
    – llrs
    Jan 18 '18 at 15:15
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If you mean that you want snps from individuals, instead of all together, you can find them in 1000 genomes. Here different individuals from different populations are sequenced and variants are called, including snps.

Maybe you should add to your question what your goal is, what would you like to find?

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  • $\begingroup$ Actually I am an engineer and new to bioinformatics. I am currently working on how to achieve data privacy on genomic data, for which I need human SNPs data. Like I need SNPs data for at least 100 humans. Where can I find only human SNPs data? $\endgroup$
    – user2210
    Jan 23 '18 at 19:16
  • $\begingroup$ Did you take a look at 1000G? You can find snps of a 1000 humans! $\endgroup$
    – benn
    Jan 23 '18 at 19:42
  • $\begingroup$ Yes, this is the link in 1000G where I am looking ftp-trace.ncbi.nih.gov/1000genomes/ftp/data. I am not able to see any SNP sequences here. Can you please provide me the exact link if possible. $\endgroup$
    – user2210
    Jan 23 '18 at 21:33
  • $\begingroup$ You are looking at alignments now, I guess you want the variants called already? Look for the VCF files, like here. $\endgroup$
    – benn
    Jan 23 '18 at 22:03
  • $\begingroup$ Thanks for the response!! I am not fully aware about the technical terms in bio. Can you please provide some information about the alignments and the variants? How to distinguish between them? $\endgroup$
    – user2210
    Jan 24 '18 at 17:19

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