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Old 01-27-2012, 05:52 AM   #1
adrian
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Location: baltimore

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Default Where can I get GM19240 HapMap cell line variant calls as VCF or a BED file

Hi:
I am urgently looking for all the variant calls in either BED or VCF file for
GM19240 and GM12878 HapMap cell lines.
Could any one point me to sites where I can download all variant calls both SNPs and Indels for these two cell lines.

thank you. Appreciate your help.

-Adrian
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Old 01-27-2012, 06:52 AM   #2
sdvie
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Default

I found this link where you can apparently download the entire latest hapmap build in vcf format (for sites and genotypes):

ftp://ftp.broadinstitute.org/bundle/...9.sites.vcf.gz

ftp://ftp.broadinstitute.org/bundle/....3.hg19.vcf.gz

I did not download it but I suppose you can then filter out the information for the samples you are interested in.

Cheers,
Sophia

PS.: In the table, the corresponding sample ID prefixes are NA- instead of GM- .

Last edited by sdvie; 01-27-2012 at 07:21 AM.
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Old 09-13-2012, 01:27 AM   #3
salturki
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Default

Thank you Sophia.

For some reason, I couldn't access the FTP site directly. However, the following helped to get access those files:

ftp://gsapubftp-anonymous@ftp.broadi...ndle/1.2/hg19/
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