Closed biozzq closed 3 years ago
Hi there,
Based on the log output, it looks like over 95% of the windows with <=301 scores had 0 xpnsl scores <-2.
Low Scores
nSNPs 1.0 5.0
301 0.0849607 0
Unfortunately when this is the case, 95% of scores are less than or equal to 0 and 0 gets chosen as the threshold for the top 5% of windows with high proportions of negative scores in the 301 bin. Clearly these regions aren't particularly interesting given that ALL windows in the 301 bin would be classified as in the top 5%. I would probably increase your window size in this case, since on the flip side there seem to be quite a lot of windows in the 301 bin with lots of xnpsl scores >2.
High Scores
nSNPs 1.0 5.0
301 0.995025 0.430535
Hi @szpiech
Thank you.
Best,
Dear @szpiech
Regarading the following two windows, the fraction scores gt/lt threshold are all 0, however these two windows are in the top5 results of the ref population. In addition, the absolute of the min scores for these two windows are all lt 2. I normalized all chromosomes jointly (norm --xpnsl --bp-win --winsize 20000 --files *.out), I do not why these two windows can be treated as the top5 results in ref population. Thanks for your help in advance.