Recent changes to GenerateGRM

GenerateGRM modified by Guobo Chen

Guobo Chen — Wed, 05 Mar 2014 12:26:04 -0000

--- v4
+++ v5
@@ -38,15 +38,26 @@
 The first two columns point to the rows of this pair of individuals in the *.grm.id file, in which their identifiers, as defined in the *.fam, can be found.

 **--Example**
+
+~~~~~
 gear --bfile test --make-grm --out test
 gear --bfile test --make-grm-txt --out test
 gear --bfile test --make-grm --ref-freq freq --out test
 gear --bfile test --make-grm --maf-range 0.4,0.6 --out test
 gear --bfile test --make-grm --grm-range 100,200 --out test
+~~~~~

 If use grm-partition option
+
+~~~~
 gear --bfile test --make-grm --grm-partition 10 --out test --name test
+~~~~
+
 It will generate 10 shell scripts, test.1.sh, test.2.sh, ..., test.10.sh.
 In the first script, say test.1.sh, it reads as below
+
+~~~~
 gear --bfile test --make-grm --grm-range x,y --out test.1
+~~~~
+
 GEAR will automatically set the numbers to the option --grm-range.

GenerateGRM modified by Guobo Chen

Guobo Chen — Thu, 18 Apr 2013 12:55:02 -0000

--- v3
+++ v4
@@ -12,7 +12,6 @@
 --grm-range
 Specify the range of the individual pairs that the grm scores will be generated.  For example, --grm-range 100,200 only generates grm scores for the 100th to the 200th pairs.

-
 --ref-freq
 Specifies the reference allele frequencies for generating genetic relatedness scores.  The format for the frequency file reads below.

@@ -25,6 +24,8 @@
 --maf-range
 Specifies the range (inclusive) of the minor allele frequencies.  Only SNPs within this range will be used for generating genetic relatedness scores.  If the reference allele frequency, f, is greater than 0.5, say 0.65, it will be converted to 1-f.

+--grm-partition
+This option partitions the whole grm into k even subdivisions, each of which will be submitted to the HPC.

 There are four columns in the grm, in either gz or grm format, is as defined below (no title line included).

@@ -42,3 +43,10 @@
 gear --bfile test --make-grm --ref-freq freq --out test
 gear --bfile test --make-grm --maf-range 0.4,0.6 --out test
 gear --bfile test --make-grm --grm-range 100,200 --out test
+
+If use grm-partition option
+gear --bfile test --make-grm --grm-partition 10 --out test --name test
+It will generate 10 shell scripts, test.1.sh, test.2.sh, ..., test.10.sh.
+In the first script, say test.1.sh, it reads as below
+gear --bfile test --make-grm --grm-range x,y --out test.1
+GEAR will automatically set the numbers to the option --grm-range.

GenerateGRM modified by Guobo Chen

Guobo Chen — Wed, 17 Apr 2013 12:50:53 -0000

--- v2
+++ v3
@@ -9,11 +9,22 @@
 --make-grm-txt
 Generates genetic relationship scores and save the output in text format.  Two output files are generated under this option: *.grm.txt, and *.grm.id.

+--grm-range
+Specify the range of the individual pairs that the grm scores will be generated.  For example, --grm-range 100,200 only generates grm scores for the 100th to the 200th pairs.
+
+
 --ref-freq
-Specifies the allele frequency for generating genetic relatedness scores.
+Specifies the reference allele frequencies for generating genetic relatedness scores.  The format for the frequency file reads below.

---freq-range
-Specifies the range (inclusive) of the allele frequencies.  Only SNPs within this range will be used for generating genetic relatedness scores.
+CHR | SNP | A1 | A2 | freq(A1) | NCHR
+----|-----|----|----|----------|-----
+1 | rs0 | A | C | 0.488 | 1000
+1 | rs1 | A | C | 0.477 | 1000
+1 | rs2 | C | A | 0.469 | 1000
+
+--maf-range
+Specifies the range (inclusive) of the minor allele frequencies.  Only SNPs within this range will be used for generating genetic relatedness scores.  If the reference allele frequency, f, is greater than 0.5, say 0.65, it will be converted to 1-f.
+

 There are four columns in the grm, in either gz or grm format, is as defined below (no title line included).

@@ -29,4 +40,5 @@
 gear --bfile test --make-grm --out test
 gear --bfile test --make-grm-txt --out test
 gear --bfile test --make-grm --ref-freq freq --out test
-gear --bfile test --make-grm --freq-range 0.4,0.6 --out test
+gear --bfile test --make-grm --maf-range 0.4,0.6 --out test
+gear --bfile test --make-grm --grm-range 100,200 --out test

GenerateGRM modified by Guobo Chen

Guobo Chen — Tue, 16 Apr 2013 11:08:59 -0000

--- v1
+++ v2
@@ -8,6 +8,12 @@

 --make-grm-txt
 Generates genetic relationship scores and save the output in text format.  Two output files are generated under this option: *.grm.txt, and *.grm.id.
+
+--ref-freq
+Specifies the allele frequency for generating genetic relatedness scores.
+
+--freq-range
+Specifies the range (inclusive) of the allele frequencies.  Only SNPs within this range will be used for generating genetic relatedness scores.

 There are four columns in the grm, in either gz or grm format, is as defined below (no title line included).

@@ -22,3 +28,5 @@
 **--Example**
 gear --bfile test --make-grm --out test
 gear --bfile test --make-grm-txt --out test
+gear --bfile test --make-grm --ref-freq freq --out test
+gear --bfile test --make-grm --freq-range 0.4,0.6 --out test

GenerateGRM modified by Guobo Chen

Guobo Chen — Tue, 16 Apr 2013 01:32:23 -0000

Generate genetic relationship scores

This procedure generates genetic relationship scores for individuals.

Options
--make-grm
Generates genetic relationship scores and save the output in gz (gzip) format. Two output files are generated under this option: .grm.gz, and .grm.id.

--make-grm-txt
Generates genetic relationship scores and save the output in text format. Two output files are generated under this option: .grm.txt, and .grm.id.

There are four columns in the grm, in either gz or grm format, is as defined below (no title line included).

ID1	ID2	Number of Markers	Genetic relatedness score
1	1	100	1.1
2	1	100	0.003
2	2	99	0.98

The first two columns point to the rows of this pair of individuals in the .grm.id file, in which their identifiers, as defined in the .fam, can be found.

--Example
gear --bfile test --make-grm --out test
gear --bfile test --make-grm-txt --out test