Hi all,
I have a question regarding determing if an identified SNP would be a heterozygote. When looking at the total number of reads for a specific base, what percentage of those reads need to differ from the reference to be considered a heterozygote. For example, if a base has 50 a coverage of 50 reads, but 25% of them differ from the reference would this be called as a heterozygote? Essentially, at what proportion of calls that differ from the reference is a homozygote vs. heterozygote?
Any thoughts?
thanks
I have a question regarding determing if an identified SNP would be a heterozygote. When looking at the total number of reads for a specific base, what percentage of those reads need to differ from the reference to be considered a heterozygote. For example, if a base has 50 a coverage of 50 reads, but 25% of them differ from the reference would this be called as a heterozygote? Essentially, at what proportion of calls that differ from the reference is a homozygote vs. heterozygote?
Any thoughts?
thanks
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