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Old 07-20-2017, 12:30 AM   #5
Location: chicago

Join Date: Nov 2012
Posts: 19

Originally Posted by SNPsaurus View Post
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.
Thanks for your nice method recommendation. Another problem would be how to measure the heteroplasmy level of mitochondrial DNA. Thanks!
cindylanzao is offline   Reply With Quote