0 count of count_diffs and count_comparisons and all in count_missing

[hrluo93]

Hi,

I used:
bcftools mpileup -f reference.fa -b bamlist.txt -r chr10 | bcftools call -m -Oz -f GQ -o chr10-bcf.vcf.gz to get all sites vcf

Then

I used command:
pixy --stats pi dxy fst --populations poplist2.txt --window_size 50000 --vcf chr10-bcf.vcf.gz --n_cores 2 --output_prefix chr10gipixy > chr10pixy.log

the result was NA, count_diffs and count_comparisons were both 0 and all is count_missing

I upload a small chr18 where showed the same results.

chr10pixy.log
chr18-bcf.filter.vcf.gz

poplist2.txt

Have I missing some step?

Best!

[smallfishcui]

Same here. Did you figure out the reason?

thanks,
Cui

[JeffWeinell]

I also have this problem!

[ksamuk]

This is a bug, and the current solution is to roll back to pixy 1.2.5 (all calculations are unchanged relative to the current version).

[hrluo93]

Same here. Did you figure out the reason?

thanks, Cui

Hi,
I finally used ANGSD to Calculate Dxy.

[hrluo93]

This is a bug, and the current solution is to roll back to pixy 1.2.5 (all calculations are unchanged relative to the current version).

Thanks for your reply!
I am looking forward to the pipeline for dealing sex-chromosome hemizygous region.

[hrluo93]

I also have this problem!

It seems like a bug.

[JeffWeinell]

Downgrading to pixy 1.2.5 solved it for me, thanks!

[smallfishcui]

Thanks for the answers! Downgrading to pixy 1.2.5 worked for me as well!

Cui

[smallfishcui]

This is a bug, and the current solution is to roll back to pixy 1.2.5 (all calculations are unchanged relative to the current version).

Thanks for your reply! I am looking forward to the pipeline for dealing sex-chromosome hemizygous region.

would ploidy be a problem with ANGSD?

[hrluo93]

This is a bug, and the current solution is to roll back to pixy 1.2.5 (all calculations are unchanged relative to the current version).

Thanks for your reply! I am looking forward to the pipeline for dealing sex-chromosome hemizygous region.

would ploidy be a problem with ANGSD?

Hi!

I guess that the hemizygous region would be a problem for both pixy and ANGSD. If your species were 2 ploidy or 4 ploidy but treated it as 2 ploidy two subgenome, it would not be a problem.

For ANGSD, I guess that the problem is all non-SNP sites are considered invariant sites. It is not a problem for my species because of the low ratio (~10%) of repeat sequences. But if the target species had a ratio of complex repeats, it would be a problem. As well as this opinion(https://x.com/jrossibarra/status/1753102333331042622).

[smallfishcui]

This is a bug, and the current solution is to roll back to pixy 1.2.5 (all calculations are unchanged relative to the current version).

Thanks for your reply! I am looking forward to the pipeline for dealing sex-chromosome hemizygous region.

would ploidy be a problem with ANGSD?

Hi!

I guess that the hemizygous region would be a problem for both pixy and ANGSD. If your species were 2 ploidy or 4 ploidy but treated it as 2 ploidy two subgenome, it would not be a problem.

For ANGSD, I guess that the problem is all non-SNP sites are considered invariant sites. It is not a problem for my species because of the low ratio (~10%) of repeat sequences. But if the target species had a ratio of complex repeats, it would be a problem. As well as this opinion(https://x.com/jrossibarra/status/1753102333331042622).

Thanks for sharing! It seems pixy is much more realistic with regards to treating monomorphic sites then. As far as I know, ANGSD uses site frequency spectrum to calculate the pi and theta. I just wonder how much it is differed from pixy, especially for polyploid data. And is it okay to compare with tetraploid and diploid pi? If someone can help, it's very much appreciated.

thanks,
Cui