error: unhandled exception: invalid integer: 0.065 [ValueError]

[asmlgkj]

Thanks a lot for this great tool.
I found it can cause error, if mean depth is low, for example my mean depth is 0.65, so if I want to get the 0.1x Uniformity,
command

mosdepth --fast-mode --by xx.bed -t 4 --thresholds 0.065 -Q 30
it will give such error

this situation maybe also in wgs data, which the mean depth is very low. my above example is a low quality ngs panel data

[brentp]

Hi, certainly the error message could be improved, but the help for --thresholds is:

for each interval in --by, write number of bases covered by at
                                least threshold bases. Specify multiple integer values separated
                                by ','.

so it indicates that you need to use integer values.

[asmlgkj]

yes, but if that, the integer wiill be 0, so the 0.1x Uniformity will be 100%, which is not right;
for very low sequence depth data, this can happen

[brentp]

thresholds is not the means to do what you want.
you can make a histogram of the mean depths in the 4th column of the output.regions file or you can use the summary.