Whole genome wide relatedness - gc5k/GEAR GitHub Wiki
This function provides whole genome-wide assessment for the effective number of samples and the effective number of genome segments.
Master command: grm
Options
--bfile
Specifies the binary genotype files.
--chr
Specifies the chromosome for analysis.
--maf
Specifies the threshold for minor allele frequency.
--inbred
If the data is based on selfing samples, such as Arabidopsis, it is suggested to switch this option on.
--dom
Generate genetic relationship matrix for dominance effects.
--adj-var
When this option is switched on, it uses the estimated variance of a locus to scale the genetic relationship matrix.
--vandem
When this option is switched on, it uses the expected variance of a locus to scale the genetic relationship matrix.
--thread-num
Specify the number of threads to run the analysis.
Examples
gear grm --bfile test --out test
gear grm --bfile test --dom --out test
gear grm --bfile test --chr 1 --out test
gear grm --bfile test --chr 1 --maf 0.01 --out test
gear grm --bfile test --inbred --out test
gear grm --bfile test --adj-var --out test
gear grm --bfile test --adj-var --thread-num 4 --out test
Note: "gear" refers to "java -jar gear.jar"; you can specify the memory by "java -jar -Xmx1024M gear.jar".