Hi.
I have a "VCF" file that i've created "de novo". That is, I have NOT mapped my reads to a reference genome, but rather constructed this VCF by utilizing sequence similarity. Within this VCF file, I have roughly 9000 SNPs. A small portion of these - ca 100 - I've identified as "outliers" (using other tools). I want to investigate these SNPs further and see if they are connected to a some genetic function but I don't know how to proceed. My understanding is that I need the DNA sequence where these SNPs are found, so that I may "Blast" them against other sequences in some database.
But how do I actually find the DNA sequences that I need, if I don't the ability to map the reads to a reference genome? I still have my "FASTA" files, of course, where I'm guessing the DNA sequences are found.
Thank you!
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Doing alignments if you did not do mapping? Or otherwise how did you do this.
I've used the "de novo" approach described here: https://academic.oup.com/g3journal/article/1/3/171/5986549 It checks for sequence similarity among reads, creates loci and genotypes SNPs that way.