Question: TCGA CNV/SNP6 Reference Sequence - hg19
2
gravatar for dirigible2012
4.9 years ago by
dirigible2012310
European Union
dirigible2012310 wrote:

Hello all,

The Broad Institute did the CNV analysis for the TCGA samples. The only information I have been able to find about the reference genome* does not give the version of hg19 they are using. I have two questions:

1. Is hg19 exactly the same as Ensembl's GRCh37? 

2. It looks from the Ensembl site that the data has had various patches and updates. I have a list of CNV start end co-ordinates and want to extract the genes involved. How much difference will it make if I use a version with the wrong patches?

Thanks,

Stephanie

https://confluence.broadinstitute.org/display/GDAC/FAQ#FAQ-Q Whatreferencegenomebuildareyouusing

hg19 cnv snp reference genome tcga • 2.4k views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 4.9 years ago by dirigible2012310
3
gravatar for Sean Davis
4.9 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

For the autosomes and sex chromosomes, hg19 and GRCh37 are the same.  For the purposes of start and end coordinates, the patches won't make a difference for the standard chromosomes.

ADD COMMENTlink written 4.9 years ago by Sean Davis25k
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