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Old 11-29-2017, 10:26 AM   #1
Opio
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Location: Norway

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Default UCSC / NCBI (hg19/GRCh37) : differences and standard

Hi,

new to bioinformatics
I realised today that my lab for a vcf file is using a different format that I am using usually: I'm using as a reference UCSChg19, which seems (to be confirmed) to use the following standard for chromosomes: chrx.
My lab is using the following : x .
After some time on it, it seems that my lab is using a GRCh(NCBI) standard, but it seems that all my pipeline has to be rerun with that reference.

What are the differences between the two? Is there any out of the chromosome name?
What is Ensembl in all that?
What is the fasta genome from 1000G?
Can this be converted at all?

Sorry for those silly simple-as-dead questions

Best,

opio
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Old 11-29-2017, 10:56 AM   #2
GenoMax
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Default

There should be no difference in the sequence since it is the same genome build. As you discovered, UCSC uses a "chr" prefix for chromosomes whereas Ensembl uses plain numbers (e.g. 1). Some finer information available here: https://www.biostars.org/p/119295/#119308
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