FST details (by SNP FST) not printed
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- C
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Description
Hi!
I've been trying to get FST estimates per variant. I'm using the flag "fstdetailsname" as shown below, which I thought would do that, but I still only get the overall FST estimate. I tried other configurations but so far I only get that one line of output.
I would be very grateful for any help on this :) thank you!
My par file looks as follows:
genotypename: phased_panel.snpOnly.targetPopFiltered.ped
snpname: phased_panel.snpOnly.targetPopFiltered.map
indivname: AMR_EAS_EUR_poplist.ind
poplistname: AMR_EAS.EIGEN.list
fstonly: YES
fstdetailsname: FSTdetails.out
phylipoutname: FSTmatrix.phy
Output:
Fst statistics between populations: fst fstjack std error Z snpnumber
F_st AMR EAS 0.004445 0.004445 0.000254 17.467 3595170
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
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Research direction
Start by reproducing the report with the supplied parameter file and input names, checking how fstonly and fstdetailsname are handled. Trace the FST output path to determine why only the summary line appears. Done means the same run produces the expected per-variant FST details file while retaining the overall estimate.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- c
- Domain
- bioinformatics, cli
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100