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Hello,
I am running nsgStat in different populations. No matter which population I used, when I try to get the stats by doing:
`/opt/ngsTools/ngsPopGen/ngsStat -npop 1 -postfiles BIA.unfolded.ref.po…
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Hi all,
Wondering if I can have some assistance to extract unweighted Fst in windows from my low-coverage population genomic data. I have followed the realSFS method to estimate Fst values from pop…
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Hi,
I'm trying to build a Docker container with **mlst**, but it seems not working properly.
I'm using Blast+ v2.6.0 binaries and **mlst** GitHub release v2.9 (`wget https://github.com/tseemann/ml…
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Hi,
I am trying to get a PCA plot for the whole genome. It is taking me a lot of time to generate the .geno file for the whole genome. Now I am planning to call chromosome by chromosome and merge…
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Hi ANGSD team,
when running
>realSFS fst print here.fst.idx 2>/dev/null
what is reported in column 3 and column 4 when the `*idx` file was created with `-whichFst 0` or `-whichFst 1`?
many…
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Hi,
I would like to calculate expected heterozygosity for my populations using .saf files and ngsStat, but I keep getting the error: "Possible error reading SFS, binary file might be broken".
I hav…
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Hi,
I have been following the ngsTools/TUTORIAL, in particular to try and create a tree with FastMe from .dist data generated by ngsDist. The problem is that the pdf file that R plots is 'corrupted' …
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Hi,
I have 5 domestic populations and 1 wild population
While I doMaf to get SNP position, should I do this separately (in to 6 pops)
Or
use all individuals in one single bam list (all in One pop…
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Dear all,
I use angsd and ngsTools to do PCA analysis and I found the PCA analysis (by angsd) are not similar with my previous study (by Plink). I tried lots of parameters in angsd and found the resu…
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I used below code to run, it printed a error "Possible error,binaryfiles might be broken"
/home/lvfh/Tools-Reseq/ngsTools/ngsPopGen/ngsCovar -probfile test.pops.geno -outfile test.covar -nind 10 -nsit…