I am trying looking for genetic mutations in plasma. This was done by multiplex amplicon sequencing using custom primers. Variant calling was done with a tool in the SamTools suite, called mPileup. Two filters based on the variant allele frequency (more than 0.5%) and ratio of variant to 3rd highest base ( at least 15), were used to remove low quality reads.
I am detecting very few variant reads in our plasma samples.
Does anyone have an idea why this happens? What could be a cause of this result? I am hoping to get more variants in my plasma sample
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Detection of mutations in plasma using multiplex amplicon sequencing
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