Hi all,
I’ve been working on whole exome sequencing using SureSelect and Illumina GAIIx.
I have a whole list of single nucleotide variations, certainly too many to check them all. So I was wondering if I could do some filtering. What I did was remove all variants that are present in dbSNP131. However, when I presented these data, a lot of people say that dbSNP131 is not a good measure to use. According to them, I should either use dbSNP130 or data from the 1000 genomes project.
But as for as I understand, data from the 1000 genomes project are incorporated into dbSNP (although with some delay). And how can you be sure that variants found in the 1000 genomes project are truly polymorphisms and not mutations?
What do you think of this? Can I use dbSNP130 and ‘upgrade’ the coordinates to hg19? Where to find a list of SNPs from 1000 genomes project? Or do I just continue with dbSNP131?
Any input would be greatly appreciated.
Lien
I’ve been working on whole exome sequencing using SureSelect and Illumina GAIIx.
I have a whole list of single nucleotide variations, certainly too many to check them all. So I was wondering if I could do some filtering. What I did was remove all variants that are present in dbSNP131. However, when I presented these data, a lot of people say that dbSNP131 is not a good measure to use. According to them, I should either use dbSNP130 or data from the 1000 genomes project.
But as for as I understand, data from the 1000 genomes project are incorporated into dbSNP (although with some delay). And how can you be sure that variants found in the 1000 genomes project are truly polymorphisms and not mutations?
What do you think of this? Can I use dbSNP130 and ‘upgrade’ the coordinates to hg19? Where to find a list of SNPs from 1000 genomes project? Or do I just continue with dbSNP131?
Any input would be greatly appreciated.
Lien
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