dadi-cli GenerateFS issue
Alexandra Sumarli
Dear Ryan and dadi-cli team,
I would like to use dadi-cli to generate an allele frequency specturm for a polarized vcf. However, when I plot the unfolded fs, I have been getting a plot that looks (partially?) folded and incomplete. It is attached below (on left) alongside an unfolded fs (on right) I was able to generate using easy-sfs without any issues.
Here is what I did for your reference:
1.) dadi-cli GenerateFs --vcf annotated_no_wheat_autosomes_snpeff_dadi_061224_synon.liftover.vcf.gz --pop-info pops.txt --pop-ids CB CL --projections 20 20 --polarized --output unfolded.fs
2.) dadi-cli Plot --fs unfolded.fs --output unfolded.pdf
The vcf was polarized using the program est-sfs and then annotated so that the ancestral allele (AA=) is in the INFO column. I have attached a screenshot of my vcf header below.
Because I was able to generate an unfolded sfs with easy-sfs successfully, I am unsure if this is a vcf formatting issue or something else? Ultimately, I would like to generate the fs in dadi-cli so I can perform statistical testing using GIM. I am more than happy to email you a subset of my original polarized vcf and populations file so that you might try to recreate the issue and/or see if there are issues with the vcf.
Thank you so much for your help and I look forward to hearing back from you!
Best,
Alexandra Sumarli
Ryan Gutenkunst
On Oct 9, 2024, at 12:59 PM, 'Alexandra Sumarli' via dadi-user <dadi...@googlegroups.com> wrote:
Dear Ryan and dadi-cli team,
I would like to use dadi-cli to generate an allele frequency specturm for a polarized vcf. However, when I plot the unfolded fs, I have been getting a plot that looks (partially?) folded and incomplete. It is attached below (on left) alongside an unfolded fs (on right) I was able to generate using easy-sfs without any issues.
<Screenshot 2024-10-09 at 12.35.40 PM.png><Screenshot 2024-10-09 at 12.36.25 PM.png>
Here is what I did for your reference:
1.) dadi-cli GenerateFs --vcf annotated_no_wheat_autosomes_snpeff_dadi_061224_synon.liftover.vcf.gz --pop-info pops.txt --pop-ids CB CL --projections 20 20 --polarized --output unfolded.fs
2.) dadi-cli Plot --fs unfolded.fs --output unfolded.pdf
The vcf was polarized using the program est-sfs and then annotated so that the ancestral allele (AA=) is in the INFO column. I have attached a screenshot of my vcf header below.
<Screenshot 2024-10-09 at 12.39.59 PM.png>
Because I was able to generate an unfolded sfs with easy-sfs successfully, I am unsure if this is a vcf formatting issue or something else? Ultimately, I would like to generate the fs in dadi-cli so I can perform statistical testing using GIM. I am more than happy to email you a subset of my original polarized vcf and populations file so that you might try to recreate the issue and/or see if there are issues with the vcf.
Thank you so much for your help and I look forward to hearing back from you!
Best,
Alexandra Sumarli
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<Screenshot 2024-10-09 at 12.36.25 PM.png><Screenshot 2024-10-09 at 12.39.59 PM.png><Screenshot 2024-10-09 at 12.35.40 PM.png>