singhal / popgen_tutorial Goto Github PK

Hi,
Thank you for your sharing pop_gen tutorial.
When I follow the steps, I can not find two EIG prmeter files: Massoko_smartpca.par and convert.par, as in the next two command in the toturial.

EIG-6.1.3/bin/convertf -p convert.par
~/EIG-6.1.3/bin/smartpca -p Massoko_smartpca.par > Massoko_smartpca.out

So, can you share these two files?
Thank you.

Dear Sir/Madam:
I am a bit confuse where the .map file is generated. Would u mind explain it?

EIG-6.1.3/bin/convertf -p convert.par cat Massoko_Dryad_VCF_final_subset_noIndels_maf05_thinned1K.map | awk -F'\\\s+' '{print $1,$2, $3,$4}' > map

Not sure what the purpose of the convertf part of the script.

Thanks!

I noticed that there are few python scripts used in the tutorial, e.g.,
vcf_to_phy.py --infile Massoko_Dryad_VCF_final_subset_noIndels_maf05_thinned1K.vcf.gz
vcf_to_geno.py

Do you know where I can locate them as I would like to follow your tutorial?