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

adrian · 01-27-2012, 05:52 AM

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

sdvie · 01-27-2012, 06:52 AM

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- .

salturki · 09-13-2012, 01:27 AM

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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01-27-2012, 05:52 AM	#1
adrian Member Location: baltimore Join Date: Oct 2009 Posts: 89	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

01-27-2012, 06:52 AM	#2
sdvie Member Location: Spain Join Date: Jul 2010 Posts: 68	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.

09-13-2012, 01:27 AM	#3
salturki Member Location: Cambridge, UK Join Date: May 2008 Posts: 12	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/