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Question: Where Can I Download Vcf Files For Publicly Available Data?
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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

ADD COMMENTlink 8.2 years ago Kevin • 630 • updated 5.7 years ago e.cirillo8923 • 0
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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.

ADD COMMENTlink 8.2 years ago Zev.Kronenberg 11k
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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.

ADD REPLYlink 8.2 years ago
Khader Shameer
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Hi Zev -- I'd love to have access to the 200 Danish exomes as well, would be glad to provide more details.

ADD REPLYlink 8.2 years ago
Deniz
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I believe I don't need IRB since I generated the VCF calls from raw reads that were publicly available?

ADD REPLYlink 8.2 years ago
Zev.Kronenberg
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Awesome, if ENA is not appropriate for VCF submissions, you may also try Dryad data repositiory http://datadryad.org/.

ADD REPLYlink 8.2 years ago
Khader Shameer
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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.

ADD REPLYlink 8.2 years ago
Roman Valls Guimerà
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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

ADD REPLYlink 8.2 years ago
Zev.Kronenberg
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Hi Zev, are the VCFs still available? I am interested in obtaining a copy. my email is ashkot[at]hotmail.com

ADD REPLYlink 5.2 years ago
win
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Hi Zev -- I'd love to have access to the 200 Danish exomes as well, could you send me? eyupsvs@hotmail.com

ADD REPLYlink 2.1 years ago
eyupuctepe
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can you share the file via OneDrive

ADD REPLYlink 20 months ago
tesmai4
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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
(...)
ADD COMMENTlink 8.2 years ago Pierre Lindenbaum 120k
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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?

ADD COMMENTlink 8.2 years ago Deniz • 140
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Depending on what you're trying to do, you might find Kaviar useful: --> http://db.systemsbiology.net/kaviar/

ADD COMMENTlink 8.2 years ago Gustavo • 530
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Greetings again. I have loaded the Danish Exomes to a Dropbox. Shoot me an email to get the goods :-).

ADD COMMENTlink 8.2 years ago Zev.Kronenberg 11k
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Hi could you share them with raygoza4@gmail.com. Regards

ADD REPLYlink 8.2 years ago
Raygozak
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This is great, could you also share with sptaylorUCLA@gmail.com? Thanks

ADD REPLYlink 8.1 years ago
Sptaylor
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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!)

ADD REPLYlink 8.1 years ago
Kevin
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@zev.kronenberg thanks Zev, my email is denizkural --@T-- gmail --D0T-- com I likewise finally returned to the thread, if a bit late.

ADD REPLYlink 8.1 years ago
Deniz
• 140
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Hi, if you still have it could you also share them with me? avpostma@gmail.com. many thanks.

ADD REPLYlink 7.7 years ago
avpostma
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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

ADD REPLYlink 5.3 years ago
kc.mailinglist
• 0
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Sent the link to your email.

ADD REPLYlink 5.3 years ago
Zev.Kronenberg
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is it possible to get the data to wowater@yandex.ru ? Thanks!

ADD REPLYlink 4.9 years ago
Vova Naumov
• 220
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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

ADD REPLYlink 4.8 years ago
Irene@Sequencing.com
• 230
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Hi could you share them with piechota.marcin [at] gmail.com. Thanks

ADD REPLYlink 4.8 years ago
piechota.marcin
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Hi,

I was wondering if the Danish data are still available.

Thank you

ADD REPLYlink 3.9 years ago
francesco.montinaro
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Hi Zev, Picking up quite an old thread. Is the dataset still available for download? email: tesmai4@gmail.com

ADD REPLYlink 20 months ago
tesmai4
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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!

ADD COMMENTlink 5.7 years ago e.cirillo8923 • 0

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