Question: Where Can I Download Most Updated Cnvs Of Hg19 ?
3
gravatar for biorepine
6.7 years ago by
biorepine1.4k
Spain
biorepine1.4k wrote:

Where can I download most updated Copy Number Variations in human genome (hg19) ?

cnv • 4.4k views
ADD COMMENTlink modified 7 months ago by Biostar ♦♦ 20 • written 6.7 years ago by biorepine1.4k
6
gravatar for Pierre Lindenbaum
6.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum121k wrote:

A list of the CNV's used by the GATK is available on the Broad FTP site:

"The current best set of known indels to be used for local realignment (note that we don't use dbSNP for this anymore); use both files:

1000G_phase1.indels.b37.vcf (currently from the 1000 Genomes Phase I indel calls)
Mills_and_1000G_gold_standard.indels.b37.sites.vcf"

http://gatkforums.broadinstitute.org/discussion/1213/whats-in-the-resource-bundle-and-how-can-i-get-it

ADD COMMENTlink written 6.7 years ago by Pierre Lindenbaum121k
1
gravatar for deanna.church
6.7 years ago by
deanna.church1.1k
Bethesda, MD
deanna.church1.1k wrote:

dbVar is a repository of structural variation (http://www.ncbi.nlm.nih.gov/dbvar). We routinely remap variants submitted on older assemblies to the newest ones (when we can). Data is organized by study so it is straightforward to get the data you want, both 1000 genomes and other studies.

ADD COMMENTlink written 6.7 years ago by deanna.church1.1k
2

These files are updated in 2010 (not the most updated one). http://projects.tcag.ca/variation/tableview.asp?table=DGV_Content_Summary.txt

ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by biorepine1.4k
1

These files are from DGV, not dbVar.

ADD REPLYlink written 6.7 years ago by deanna.church1.1k
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