I am trying to get all variants of all types for a sequence I put together through an assembly step followed by consensus building using a reference. Now I am looking for variants. I have used samtools/bcf/vcfutils steps and the first time I did so accidentally using contigs, which gave me a list of only indels as a result, and I can visually (IGV) verify these. then I tried to correct this and used the actual reads, again with samtools. this time I got a list of SNPs only, which again I can locate in IGV.
so now I am wondering what is going on? I was under the impression that samtools would locate both indels and SNPs using reads??? would it be legitimate to use indels found by using contigs in a write up?
the subject is a plant chloroplast sequence and in the end I will need some locations I can use in the lab to find differences between two related species. I am learning this as I go so any information even links to further information would be most appreciated.
so now I am wondering what is going on? I was under the impression that samtools would locate both indels and SNPs using reads??? would it be legitimate to use indels found by using contigs in a write up?
the subject is a plant chloroplast sequence and in the end I will need some locations I can use in the lab to find differences between two related species. I am learning this as I go so any information even links to further information would be most appreciated.
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