Recent changes to DataManager

DataManager modified by Guobo Chen

Guobo Chen — Mon, 08 Dec 2014 11:07:09 -0000

--- v4
+++ v5
@@ -25,3 +25,17 @@
 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
+~~~~~

DataManager modified by Guobo Chen

Guobo Chen — Mon, 10 Mar 2014 06:26:30 -0000

--- v3
+++ v4
@@ -2,21 +2,26 @@
 ------------------

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

-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
+**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
+~~~~~~~~~

DataManager modified by Guobo Chen

Guobo Chen — Tue, 28 Jan 2014 10:29:10 -0000

--- v2
+++ v3
@@ -2,14 +2,21 @@
 ------------------

 Options
-order-ind [args]
-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.
+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.
+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

DataManager modified by Guobo Chen

Guobo Chen — Thu, 23 Jan 2014 08:26:16 -0000

--- v1
+++ v2
@@ -1,9 +1,15 @@
 Data manager
 ------------------

-Option
+Options
 order-ind [args]
 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

DataManager modified by Guobo Chen

Guobo Chen — Tue, 21 Jan 2014 09:01:05 -0000

Data manager

Option
order-ind [args]
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