what input should I have for fineSTRUCTURE

Question

[brisilis]

Hello Everyone, I'm trying to use finestucture to identify the population structure of bacterial sequence. I have the core SNP vcf for all the strains and I don't know what input should I use. the manual is a bit confusing. Can you please help Thank you

Answer 1

[4galaxy77]

From the github page.

## Get some data in VCF format
git clone [e-mail]:danjlawson/pcapred.ref.git
cp pcapred.ref/inst/extdata/1000G_tinysubset.* .
gunzip 1000G_tinysubset.bim.gz
plink1.9 --bfile 1000G_tinysubset --recode vcf --out 1000G_tinysubset_unphased
## Process each chromosome separately:
for chr in `seq 1 22`; do
    ## First phase the data:
    java -jar $HOME/bin/beagle.28Jun21.220.jar gt=1000G_tinysubset_unphased.vcf out=1000G_tinysubset_chr$chr chrom=$chr
    ## Convert it to chromopainter format via the safe VCF route:
    gunzip 1000G_tinysubset_chr$chr.vcf.gz
    perl -Mlocal::lib ~/bin/vcf2cp.pl 1000G_tinysubset_chr$chr.vcf 1000G_tinysubset_chr$chr
    ## Make a suitable recombination map:
    makeuniformrecfile.pl 1000G_tinysubset_chr$chr.phase 1000G_tinysubset_chr$chr.rec
done
## Run a combined finestructure analysis:
## NB The format {1..22} is bash specific and you may have to list the files individually.
fs 1000G_tinysubset_test.cp -phasefiles 1000G_tinysubset_chr{1..22}.phase -idfile 1000G_tinysubset_chr1.ids -recombfiles 1000G_tinysubset_chr{1..22}.rec -go

[brisilis]

Thank you for your reply, However, I'm experiencing problems downloading the vcf format.

I've managed to make the following vcf file.

I don't know if it suitable for finestructre or should i use chromopainter? and what additional file do i need. I very confused.

[4galaxy77]

OK - maybe to start you could say what your aim is for the project. Then it will be easier to say whether you should just use ChromoPainter or fineSTRUCTURE as well.

[brisilis]

I'm trying to do microbial typing for a bacterial specie, Following some paper they do use core genome SNP, Chromopainter and finestructre. I have generated Core SNP VCF of all my samples but I don't know hot to proceed further.

Thank you for your help