Hi, I'm trying to use LoFreq for viral data (BAM), when I know there is a low-frequency SNP for example at a particular position 30.000 reads with original nt and 1500 reads containing SNP which makes ~3% frequency of a viral variant, but LoFreq is outputting no SNP found? Can someone with more experience on viral data can suggest options how to run the tool?
Question: LoFreq outputing no SNP?
2.5 years ago by
manekineko • 130
manekineko • 130 wrote:
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