Closed MarieLataretu closed 2 months ago
oh wow - so it is actually possible to get allele frequencies (AF) from medaka? This would be really nice to have... thx
It's "stolen" form Galaxy 😅 [MIT license, so all good]
After ARTIC they do the following:
medaka tools annotate --dpsp --pad 25
and then a custom python script that does things and adds a AF
INFO field
I can't say how it compares to other tools, but it's seems to be somewhat in line with what one would see in IGV.
Nice!
works on our end
AF
) for all passed and failed variantsINFO/DP>${params.min_depth} & INFO/AF>=0.3 & INFO/AF<=0.8
Relates to/fixes (?) #266
All three test profiles run successfully: