recap

day 2 of class was a success! we talked about markdown and how to create a file. because I have been noodling with this website for a bit, i decided to do some things differently from the file we made in class so i could upload it here.

I hope you’ll enjoy this small insight into my mind hahaha

oiiiiiiiii

my favorite websites

1. iNaturalist
2. discogs
3. facebook marketplace
   
   

check out my indie collection

y’all rock with tater tot hotdish???

this is a script to prune VCF files to a certain number of SNPs.

I was using this to reduce my combined VCF files to make my genome datasets more manageable at later steps

/programs/plink-1.9-x86_64-beta7/plink --vcf Primula_353super_LD_pruned_SNPs.recode.vcf --make-bed --allow-extra-chr --double-id --out Primula_genomeLD_pruned_thin

/programs/plink-1.9-x86_64-beta7/plink --bfile Primula_genomeLD_pruned_thin --thin-count 30000 --allow-extra-chr --double-id --recode --out Primula_genomeLD_pruned_thin_plink

/programs/plink-1.9-x86_64-beta7/plink --file Primula_genomeLD_pruned_thin_plink --allow-extra-chr --recode vcf --out Primula_genomeLD_pruned_thin_thinned


#gives missing proportion of loci for each individual
/local/workdir/jbl256/Installed_programs/vcftools-0.1.16/bin/vcftools --vcf Primula_genomeLD_pruned_thin_thinned.vcf --missing-indv

#average depth for each individual
/local/workdir/jbl256/Installed_programs/vcftools-0.1.16/bin/vcftools --vcf Primula_genomeLD_pruned_thin_thinned.vcf --depth 

#observed and expected heterozygosity
/local/workdir/jbl256/Installed_programs/vcftools-0.1.16/bin/vcftools --vcf Primula_genomeLD_pruned_thin_thinned.vcf --het


#create fasta file for downstream analyses
/local/workdir/jbl256/Installed_programs/vcf2phylip-2.8/vcf2phylip.py --input Primula_genomeLD_pruned_thin_thinned.vcf -f -n

#make structure file for later
/local/workdir/jbl256/Installed_programs/stacks-2.66/bin/populations -V Primula_genomeLD_pruned_thin_thinned.vcf -O ./ -M popmap.txt --threads 4 --ordered-export --structure