Viral haplotyping using pair end information
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6.1 years ago
lovett05 • 0

My samples have a pair of SNPs present in a subset of the population. Their distance from each other is such that both positions will never be covered in the same read, but there exists a subset of paired end reads where each mate in the pair will cover one. I've already used Samtools to extract those reads, but I find myself struggling with the next step

 

Given the above described subset of reads, what I need to know is the frequency at which both SNPs appear together, the frequency at which one SNP appears and not the other, and the frequency at which neither SNP appears. Is there a relatively easy way to get at that information?

Viral Haplotyping • 1.1k views
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