So I may be completely wrong here but please correct me since I'm mostly used to doing RNA splicing analysis.
I have sequenced sheared DNA from about 10 NA12878 cells using Illumina and a library prep that uses a non proof reading polymerase so we expect it to introduce lots of errors even early on. What I would like to do is figure out how many false positives it gives me (Allele frequency of >=15%.
To do that I need the NA12878 ref genome, and it's dbSNP database for heterozygous loci. Right? If I just align to NA12878 then the het loci that are endogenous "SNPs" would look as false positives. Where can I find the NA12878 specific dbSNP?
If there is another more logical way of doing this analysis please feel free to call me out.
Thank you!
I have sequenced sheared DNA from about 10 NA12878 cells using Illumina and a library prep that uses a non proof reading polymerase so we expect it to introduce lots of errors even early on. What I would like to do is figure out how many false positives it gives me (Allele frequency of >=15%.
To do that I need the NA12878 ref genome, and it's dbSNP database for heterozygous loci. Right? If I just align to NA12878 then the het loci that are endogenous "SNPs" would look as false positives. Where can I find the NA12878 specific dbSNP?
If there is another more logical way of doing this analysis please feel free to call me out.
Thank you!
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