stephenturner

#!/usr/bin/perl

# 2010-11-11 
# (c) Stephen Turner
# http://GettingGeneticsDone.blogspot.com/
# http://www.stephenturner.us/

# This script takes as input the base filename of binary pedfiles (*.bed, 
# *.bim, *.fam) and a base output filename and splits up a dataset by 
# chromosome. Useful for imputing to 1000 genomes. 

stephenturner

#!/usr/bin/env perl

# runs step 0 on all chromosomes
# produces the group files and the tarballed
# sets for running step1 and step 2 on

use strict;

# create and store distributions for the top 25 models from permutation testing
# for both the model p-value and interaction p-value

stephenturner

#!/bin/bash

# For running step0 of the imputation procedure 
# Splits files and creates random subset for step 1 of imputation

# adapted from original script written by Jacki Buros


# arguments are 
# 1) plink bed source file

stephenturner

#!/usr/bin/env perl

# runs step 1 on all chromosomes
# produces the input for step 2 results
# submits a pbs job for every chromosome specified

use strict;

# create and store distributions for the top 25 models from permutation testing
# for both the model p-value and interaction p-value

stephenturner

#!/bin/bash

#PBS -M youremailaddress@domain.com
#PBS -m abe
#PBS -S /bin/bash 
#PBS -l nodes=1:ppn=1
#PBS -W x=NODESET:FIRSTOF:FEATURE:opteron:x86
#PBS -l walltime=96:00:00
#PBS -l cput=96:00:00
#PBS -l pmem=8000mb

stephenturner

#!/bin/bash

#PBS -M youremailaddress@domain.com
#PBS -m abe
#PBS -S /bin/bash 
#PBS -l nodes=1:ppn=1
#PBS -W x=NODESET:FIRSTOF:FEATURE:opteron:x86
#PBS -l walltime=96:00:00
#PBS -l cput=96:00:00
#PBS -l pmem=3000mb

stephenturner

#!/bin/bash
#
# Jacki Buros
# Step 1 impute

# check params
if [ -z $prefix ]
then
	echo "$(date) | param 'prefix' not defined. Exiting."
	return $ERR_DELETE_FILES

stephenturner

plink --bfile basename --read-freq mymafs.frq --genome --min 0.05 --genome-lists tmp.list001 tmp.list001 --out data.sub.1.1
plink --bfile basename --read-freq mymafs.frq --genome --min 0.05 --genome-lists tmp.list001 tmp.list002 --out data.sub.1.2
plink --bfile basename --read-freq mymafs.frq --genome --min 0.05 --genome-lists tmp.list001 tmp.list003 --out data.sub.1.3
plink --bfile basename --read-freq mymafs.frq --genome --min 0.05 --genome-lists tmp.list001 tmp.list004 --out data.sub.1.4
plink --bfile basename --read-freq mymafs.frq --genome --min 0.05 --genome-lists tmp.list002 tmp.list002 --out data.sub.2.2
plink --bfile basename --read-freq mymafs.frq --genome --min 0.05 --genome-lists tmp.list002 tmp.list003 --out data.sub.2.3
plink --bfile basename --read-freq mymafs.frq --genome --min 0.05 --genome-lists tmp.list002 tmp.list004 --out data.sub.2.4
plink --bfile basename --read-freq mymafs.frq --genome --min 0.05 --genome-lists tmp.list003 tmp.list003 --out data.sub.3.3
plink --bfile basename --read-fr

stephenturner

#!/usr/bin/perl
#
#Parses a .fam file and generates N number of sample list files depending on 2nd argument
#Generates PBS cluster submission files
#Justin Giles, Vanderbilt University, 2010
#
use strict;

if(scalar(@ARGV) != 3){
	print "\nPLEASE NOTE: EDIT THIS SCRIPT IN THE PBS AREA TO MODIFY IT TO YOUR NEEDS\n";

stephenturner

#!/usr/bin/perl

use strict;

if(scalar(@ARGV) != 1){
	print "submit_ibd_pbs.pl <num_pbs_to_submit>\n";
	exit;
}

my $LIMIT = $ARGV[0];