popgenWindows.py Dxy estimates are large with vcf with invariant sites about genomics_general HOT 7 CLOSED

Hi Matteo,
Are your values higher or lower than you expected (I think you left out a word)?
People often see very high values using my script when invariant sites are excluded, but if yours includes invariants, there is no reason to expect a difference. We have found very similar numbers to those from pixy for example.
Simon

from genomics_general.

Hi Simon,

yes, I did leave out a word! I meant higher. The problem is that I am getting similar estimates when using both vcfs with and without invariant sites. I wonder whether filtering (e.g. max-missingness, maf...) might have something to do with this?

Matteo

from genomics_general.

Hi Matteo,
Sorry for the delay. This is very strange. If you send me a small subset of your input files (with and without invariants) I can try to diagnose what is happening.
Simon

from genomics_general.

Hi Martin,

Sure, I have uploaded the subsets here:
https://drive.google.com/drive/folders/1S62j7N1gy7I8j211u49AKx0WXKXSjVzT?usp=sharing

Best,
Matteo

from genomics_general.

Hi Matteo,
Your "all sites" file does not contain invariant sites.

#CHROM	POS	ID	REF	ALT
SUPER_25	24381	.	T	C
SUPER_25	104391	.	T	G
SUPER_25	104404	.	T	G
SUPER_25	107757	.	T	G

Note that each site has both a reference and alternate allele, and all the thousands of positions between these variants are not present.

from genomics_general.

Hi Simon,

Sorry for the delay in the response, but I wanted to make sure I ran everything correctly. I ran the pipeline again and made sure the file actually contains invariant sites as well, and after running your script I now get the expected values of Dxy. Thank you for your help and sorry for bothering you with this!!

Matteo

from genomics_general.

Hi Matteo,
Great - thanks for confirming.
All the best!

from genomics_general.