Standard deviation warning

[bjhunt-git]

Hi, thanks for making TEFLoN, I'm hoping it'll be very useful for my project.

I have a set of libraries with insert size standard deviation consistently over 100 - this is 150bp paired end reads generated on a Novoseq 6000. When running teflon.v0.4.py I get the following warning:

Insert size standard deviation estimated as 140. Use the override option if you suspect this is incorrect!
!!! Warning: insert size standard deviation reported as 140 !!!
Please ensure this is correct and use the override option!

I can get it to run using the suggested -sd option, but I was just wondering what the reason was why teflon warns about this scenario, and if I should expect any impact on the results? Does a larger insert SD affect the ability to identify TE insertion/deletions?

[heidihyang]

Hi, I would like to add onto this issue. After using the reference including mapped TEs, the stdev went up from 101 (original bam aligned to original reference) to 889 (new bam aligned to new reference). Is 889 an abnormally large stdev for insert size? Thank you!