Reference genome-SNP calling

melNGS · 09-27-2012, 04:32 AM

Hello everyone,
I'm doing resequencing using Illumina technology. I recently analysed my NGS data with NextGene software, but I got some weird SNP calling. Basically the software called a lot of homozygous SNPs that they weren't really SNPs because they were common in the population in according with dbSNPs. That result makes me think that in the reference genome (GrCh37/hg19) there is the non common allele instead to the common one...
I was wondering if someone else had the same result. How did you explain that?

Thanks a lot!

Melissa

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09-27-2012, 04:32 AM	#1
melNGS Member Location: London Join Date: Apr 2012 Posts: 12	Reference genome-SNP calling Hello everyone, I'm doing resequencing using Illumina technology. I recently analysed my NGS data with NextGene software, but I got some weird SNP calling. Basically the software called a lot of homozygous SNPs that they weren't really SNPs because they were common in the population in according with dbSNPs. That result makes me think that in the reference genome (GrCh37/hg19) there is the non common allele instead to the common one... I was wondering if someone else had the same result. How did you explain that? Thanks a lot! Melissa