Command-line Recipes#

A bunch of command-line examples provided without much explanation. See the Tutorials or other documentation for full explanations.

.vcf.gz to GRG#

# Make sure my_input.vcf.gz is tabix indexed!
grg construct -j 6 my_input.vcf.gz -o my_input.grg

.vcf.gz to IGD#

# Make sure my_input.vcf.gz is tabix indexed!
igdtools -j 6 my_input.vcf.gz -o my_input.igd

IGD to GRG#

# Will always be faster than the .vcf.gz conversion
grg construct -j 6 my_input.igd -o my_input.grg

View info about GRG#

grg process stats my_input.grg

Split GRG into pieces#

# Each resulting GRG will be a 5MB of the genome, with all the samples
grg split -s 5000000 my_input.grg

Perform GWAS#

grg assoc -p my_phenotype.phen my_input.grg -o my_input.assoc.tsv

Perform PCA#

# Get the top 20 PCs
grg pca -d 20 my_input.grg

Filter by list of individual IDs#

# list_of_individuals.txt has one ID per line
grapp filter -S list_of_individuals.txt my_input.grg my_input.filtered.grg

Show the individual IDs#

grapp show -S my_input.grg

GRG to IGD#

# This can be slow! Use more threads (-j) if possible
grapp export -j 4 my_input.grg --igd exported.igd