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Where Can I Download Vcf Files For Publicly Available Data?

I have the 1000 genomes VCF, but I am wondering if there are VCF files avail for other genomes like

  1. Korean genomes
  2. African genomes
  3. Venter
  4. Watson

Cheers

vcf snp
• 23,758 views • link
updated by Ram Ram • written by Kevin Kevin

6 answers

Complete genomics has some publicly available datasets. I am sure there is a converter to VCF. If you have an FTP server, webspace or somehow to share data, I would be happy to send you the 200 Danish exomes in VCF.

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written by Zev.Kronenberg Zev.Kronenberg

Hi Zev -- I'd love to have access to the 200 Danish exomes as well, would be glad to provide more details.

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written by Deniz Deniz

Hi Zev: I am interested in the dataset too. If you have permissions (including IRB and institutional approval), it will be nice if you can upload the data to a public data repositories like European Nucleotide Archive (http://www.ebi.ac.uk/ena/data/search/) or similar resources and share the URL here.

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written by Khader Shameer Khader Shameer

I believe I don't need IRB since I generated the VCF calls from raw reads that were publicly available?

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written by Zev.Kronenberg Zev.Kronenberg

Hi Zev, Kevin... what about publishing the Danes VCF's it into http://gigadb.org/ ? I've been told that the Danes VCF's were processed in collaboration with BGI, maybe it makes sense to have it there then.

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written by Roman Valls Guimerà Roman Valls Guimerà

Greetings,

I don't want to upload these data to a site where I might be confused as being involved in the project. I have the VCFs all ready to go... any other suggestions?

our pipeline:

BWA SAMTOOLS PICARD - dedup GATK - INDEL realign SAMTOOLS - call variants

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written by Zev.Kronenberg Zev.Kronenberg

Hi Zev, are the VCFs still available? I am interested in obtaining a copy. my email is ashkot[at]hotmail.com

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written by win win

Hi Zev -- I'd love to have access to the 200 Danish exomes as well, could you send me? eyupsvs@hotmail.com

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written by eyupuctepe • eyupuctepe

can you share the file via OneDrive

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written by tesmai4 • tesmai4

The SNPs for those genomes are available for download at the UCSC under the name "pg*" you could generate those VCF files using awk. Something like:

$ curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/pgVenter.txt.gz" |\
gunzip -c |\
awk 'BEGIN { printf("#CHROM\tPOS\tID\tREF\tALT\n");} { printf("%s\t%d\t.\t.\t%s\n",$2,1+int($3),$5);}'

#CHROM  POS ID  REF ALT
chr1    65745   .   .   G
chr1    65797   .   .   C
chr1    65872   .   .   G
chr1    66008   .   .   G
chr1    66162   .   .   T
chr1    66258   .   .   G
chr1    66275   .   .   T
chr1    66294   .   .   TA/AT
chr1    66312   .   .   T
chr1    566139  .   .   A/C
(...)
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written by Pierre Lindenbaum Pierre Lindenbaum

VCF is a very flexible format & I would be careful converting Complete Genomics directly into VCF on your own -- for example Complete handles complex variants very differently compared to how 1000G handled them in the Pilot phase. Digging into the supplemental information on the Korean genome publication etc. can help fill some of those extra fields.

Also, the genomes you've mentioned contain Structural Variation data of various degrees of completeness -- and VCF files do exist for these kinds of variants as well.

By VCF file, do you mean you're interested in the format itself, or a particular kind of variant?

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written by Deniz Deniz

Depending on what you're trying to do, you might find Kaviar useful: --> http://db.systemsbiology.net/kaviar/

• 224 views • link
written by Gustavo Gustavo

Greetings again. I have loaded the Danish Exomes to a Dropbox. Shoot me an email to get the goods :-).

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written by Zev.Kronenberg Zev.Kronenberg

Hi could you share them with raygoza4@gmail.com. Regards

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written by Raygozak Raygozak

This is great, could you also share with sptaylorUCLA@gmail.com? Thanks

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written by Sptaylor • Sptaylor

Thanks! Zev! sorry for the late reply. somehow the email notifications didn't work and I hadn't realised my question was replied. I was actually more interested in WGS VCFs thanks for your offer though. Will keep in mind when I am doing exome next (soon!)

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written by Kevin Kevin

@zev.kronenberg thanks Zev, my email is denizkural --@T-- gmail --D0T-- com I likewise finally returned to the thread, if a bit late.

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written by Deniz Deniz

Hi, if you still have it could you also share them with me? avpostma@gmail.com. many thanks.

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written by avpostma • avpostma

Hi Zev,

I'm also very interested on the 200 Danish exomes in VCF as the SRA access is no longer valid. Could you please share them with coucou90@gmail.com?

Regards
Kirsley

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updated by Ram Ram • written by kc.mailinglist • kc.mailinglist

Is it possible to get the data to wowater@yandex.ru? Thanks!

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updated by Ram Ram • written by Vova Naumov Vova Naumov

Hi Zev - please share the download link with me, too! This is really nice of you to provide, thank you. Email is irene@sequencing.com

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written by Irene@Sequencing.com Irene@Sequencing.com

Hi could you share them with piechota.marcin [at] gmail.com. Thanks

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updated by Ram Ram • written by piechota.marcin piechota.marcin

Hi Zev, Picking up quite an old thread. Is the dataset still available for download? email: tesmai4@gmail.com

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written by tesmai4 • tesmai4

Dear Zev, I'm also really interested on the 200 Danish exomes in VCF. Is still possible share it?

My email is: elisa.cirillo@maastrichtuniversity.nl

Thank you very much!

• 0 views • link
updated by Ram Ram • written by e.cirillo8923 • e.cirillo8923

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