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Old 07-06-2017, 04:13 PM   #3
SNPsaurus
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Location: Eugene, OR

Join Date: May 2013
Posts: 521
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SNP callers like Lo-Freq are meant for mixed populations. We used it when developing PELE-Seq (paired-end low error sequencing) which is a wet lab approach to detecting low frequency mutations. We examined cancer mitochondrial genotypes and were able to detect sub-population heteroplasmy. You could detect heteroplasmy with just Lo-Freq, but would need to discard SNPs below ~1-5% depending on the read depth and quality.
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