The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
what does the minReadsPerAlignmentStart argument in HaplotypeCaller mean?
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?