Dear All,
I'm dealing with some sequencing data coming from an Illumina platform and assembled on a reference genome. We employed standard filters to reduce gaps (and therefore false mismatches), but still I'm finding numerous adjoining SNPs in the dataset. I'm afraid these could be artifacts caused by reads assembly; people in bibliography present some contrasting opinions, sometimes considering these kind of SNPs as regular (and valuable) data, some other times getting rid of them.
What I'd like to ask you is if anybody supports biological reasons at the base of adjoining SNPs formations ore else if there is any filtering tool devoted to this problem. I could brutally eliminate these SNPs from the dataset, but maybe somebody came up with a more elegant way .
I'm dealing with some sequencing data coming from an Illumina platform and assembled on a reference genome. We employed standard filters to reduce gaps (and therefore false mismatches), but still I'm finding numerous adjoining SNPs in the dataset. I'm afraid these could be artifacts caused by reads assembly; people in bibliography present some contrasting opinions, sometimes considering these kind of SNPs as regular (and valuable) data, some other times getting rid of them.
What I'd like to ask you is if anybody supports biological reasons at the base of adjoining SNPs formations ore else if there is any filtering tool devoted to this problem. I could brutally eliminate these SNPs from the dataset, but maybe somebody came up with a more elegant way .
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