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what does the minReadsPerAlignmentStart argument in HaplotypeCaller mean?

Lucy_genLucy_gen SheffieldMember

The minReadsPerAlignmentStart argument in HaplotypeCaller is described as the minimum number of reads with the same alignment start for each location in an active region and has a default of 10. For each location, there will be lots of different alignment start sites (if this means the most 5' position of a read). So does this mean in each case there must be at least 10 reads sharing that 5' position? This seems a lot to me if the depth was about 30, and given that duplicates will be excluded. Can you please explain?


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