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xiaoming-liu / stairway-plot-v2

The stairway plot is a method for inferring detailed population demographic history using the site frequency spectrum (SFS) from DNA sequence data.
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Confused about which SFS numbers to use #17

Open Erikacj opened 6 months ago

Erikacj commented 6 months ago

From the angsd realSFS output I get 29 numbers from 14 individuals. Stairway Plot wants 2n-1 for unfolded SFS, so 27 numbers. Which numbers do I ignore, the first and last numbers?

2553445.800865 103809.213969 43688.859571 28674.860202 21990.861158 17054.914529 14721.903145 12352.277563 11707.233481 10945.865687 11070.809709 10355.972034 10011.312219 9803.119318 9387.831696 5617.122029 4253.325799 2615.508075 2468.261782 1593.288319 1148.791966 1317.130954 1039.779926 1126.637310 1217.816215 1393.024173 1699.225106 2439.155779 18558.097422

elizeng commented 6 months ago

Yup you ignore the first and last as they are invariable sites

Erikacj commented 6 months ago

Thank you!

timurrxxcd commented 1 month ago

@Erikacj hello, did you use first number (2553445.800865) as L input?