Human 1000genomes is using GRCh37 based reference (three steps to generate the reference fasta file, ensembl 56), but the reference snp is from dbsnp129 mapped to NCBI36.3 (built in Aug, 2009)
dbsnp130 was built on May 03, 2009, any reason dnsnp130 was not chosen by 1000genome? Is it matter that using NCBI36.3 for snp while NCBI37 for genome?
SNP annotation from Ensembl variation 56 is different with the NCBI dbsnp130 annotation (position may be different), I'm not sure the fasta file 1000genomes used is the same with NCBI37 /hg19 genome
Since hg18 (NCBI36.1) is a heavily used genome reference, there are some published results can be used for comparison, but more and more results are coming from 1000genomes, I'm confused which version of reference to use.
Any suggestion?
dbsnp130 was built on May 03, 2009, any reason dnsnp130 was not chosen by 1000genome? Is it matter that using NCBI36.3 for snp while NCBI37 for genome?
SNP annotation from Ensembl variation 56 is different with the NCBI dbsnp130 annotation (position may be different), I'm not sure the fasta file 1000genomes used is the same with NCBI37 /hg19 genome
Since hg18 (NCBI36.1) is a heavily used genome reference, there are some published results can be used for comparison, but more and more results are coming from 1000genomes, I'm confused which version of reference to use.
Any suggestion?
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