DataManager

Data manager

Options

order-ind [arg]
Order individuals as shown in order.txt. Only matched individuals will be printed out. It is a more powerful option than --keep, which does not order individuals. It only works with --make-bed. Example

gear --bfile test --order-ind order.txt --make-bed --out test_od

remove-atgc
Remove loci their alleles are A/T or G/C. Example

gear --bfile test --remove-atgc --make-bed --out test_noatgc

zero-geno [arg]
Specify the missing rate for the data. By changing the seed, the missing genotypes can be different in each run. Example

gear --bfile --zero-geno 0.05 --make-bed --out test_zero
gear --bfile --zero-geno 0.05 --make-bed --seed 2014 --out test_zero

comsnp
Extract consensus SNPs from multiple bfiles.

gear comsnp --bfiles bfile1 bfile2 --test
gear comsnp --batch batch.txt --out

In batch.txt, it reads

bfile1
bfile2