mfumagalli
commented
11 months ago Hi Sabhrina,
you should use the latest implementation of FST in ANGSD which is based on this more recent paper https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giac032/6586813 It is more efficient and possibly precise. ngsPopGen is not actively maintained.
However, ngsPopGen and ANGSD are not expected to give very different estimates of FST. You should check the effect of priors in ANGSD (are you using the 2d-sfs?) to see if that changes your distribution of FST values.
Matteo
From: Sabhrina Aninta @.> Sent: 06 November 2023 3:47 PM To: mfumagalli/ngsPopGen @.> Cc: Subscribed @.***> Subject: [mfumagalli/ngsPopGen] ngs2dSFS and ngsFst giving "Possible error reading SFS, binary file might be broken..." even after using old SAF (Issue #11)
Hi Matteo,
I was trying ngsFst for getting some Fst estimates that was mentioned in this paperhttps://doi.org/10.1534/genetics.113.154740. My motivation trying this was I can't find any clean outlier from two populations that are supposed to be different when using other Fst estimators in ANGSD.
So what I did was this:
~/bin/ngsPopGen/ngsFST -postfiles wildPop.folded.oldsaf.gz domesticPop.folded.oldsaf.gz -priorfile wildPop.domePop.unfolded.2dsfs -outfile wildPop.domePop.ngsFST -nind 17 39 -nsites 100000 -verbose 1
The .oldsaf.gz files were coming from realSFS print -oldfile 1 as was said in the "Using NGStools/NGSpopgen" section of this pagehttp://www.popgen.dk/angsd/index.php/RealSFS. The .2dsfs file was coming from realSFS of the saf.idx of the 2 populations used there. The wildPop has 17 diploid individuals and the domesticPop has 39 diploid individuals.
The message I get is this
->Dumping file: wildPop.domePop.ngsFST
->Using some of these args: -nind 56 -nind1 17 -nind2 39 -nsites 100000 -postfiles wildPop.folded.oldsaf.gz domesticPop.folded.oldsaf.gz -priorfiles (null) (null) -priorfile wildPop.domePop.unfolded.2dsfs -outfile wildPop.domePop.ngsFST -verbose 1 -firstbase 1 -block_size 20000Reading 2D prior... num win 5 win0 is 0 19999 Block 0 out of 4 from 0 to 19999
-> Possible error reading SFS, binary file might be broken...I thought that was because the 2dSFS not right (unfolded 2DSFS made with ANGSD) so I change into folded 2DSFS made with ANGSD. The message I got was still the same.
Then I was trying to make a 2D SFS file using ngs2dsfs:
~/bin/ngsPopGen/ngs2dSFS -postfiles wildPop.folded.oldsaf.gz domesticPop.folded.oldsaf.gz -outfile wildPop.domePop.ngs2dSFS -nind 34 78 -nsites 100000 -relative 1
-> Possible error reading SFS, binary file might be broken...Still the same message.
Do you know how can I get ngsFst working?
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sagitaninta
Hi Matteo,
I was trying ngsFst for getting some Fst estimates that was mentioned in this paper. My motivation trying this was I can't find any clean outlier from two populations that are supposed to be different when using other Fst estimators in ANGSD.
So what I did was this:
The .oldsaf.gz files were coming from realSFS print -oldfile 1 as was said in the "Using NGStools/NGSpopgen" section of this page. The .2dsfs file was coming from realSFS of the saf.idx of the 2 populations used there. The wildPop has 17 diploid individuals and the domesticPop has 39 diploid individuals.
The message I get is this
I thought that was because the 2dSFS not right (unfolded 2DSFS made with ANGSD) so I change into folded 2DSFS made with ANGSD. The message I got was still the same.
Then I was trying to make a 2D SFS file using ngs2dsfs:
Still the same message.
Do you know how can I get ngsFst working?