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• Module Name: xwas (see the modules page for more information)
• Environment variables set:
  • Reference data in /fdb/xwas/
  • $XWAS_BIN
  • $XWAS_IMPUTE_BIN
  • $XWAS_DB
  • $XWAS_TEST_DATA
  • $XWAS_TEST_DATA_IMPUTE

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144]$ module load xwas
[+] Loading xwas 3.0
[user@cn3144]$ # copy the input data
[user@cn3144]$ cp -r ${XWAS_TEST_DATA_IMPUTE} .
[user@cn3144]$ # create required directories
[user@cn3144]$ mkdir -p example_X_final example_X_step1 example_X_step2
[user@cn3144]$ # create a parameter file; note that trailing slashes are required
[user@cn3144]$ cat > example.par <<END_OF_CONFIG
FILE: hapmap3_euro_all
OUTPUT: hapmap3_chr23_imputed
NJOBS: 31
BUILD: 18
FILELOC: example_X_loc/
REFLOC: ${XWAS_DB}/impute_ref/
TOOLSLOC: ${XWAS_IMPUTE_BIN}/
RESLOC1: example_X_step1/
RESLOC2: example_X_step2/
FINALRESLOC: example_X_final/
MAFRULE: EUR.MAF<=0.005
END_OF_CONFIG

[user@cn3144]$ # create all the scripts
[user@cn3144]$ make_imputation_files example.par
[user@cn3144]$ # run first step; output will be in RESLOC1
[user@cn3144]$ ./hapmap3_euro_all_preimpute.sh
[user@cn3144]$ # run step 2 - run in parallel using swarm
[user@cn3144]$ swarm -t1 -p2 -g2 --time=60 -f hapmap3_euro_all_impute2_run_all.sh
[user@cn3144]$ # wait for swarm to finish
[user@cn3144]$ # run step 3
[user@cn3144]$ ./hapmap3_euro_all_impute2_cat.sh

Then run the post-impute QC pipeline. Note that build is now 19.

[user@cn3144]$ cd example_X_final
[user@cn3144]$ cat > qc.par <<END_OF_CONFIG
filename hapmap3_chr23_imputed
xwasloc ${XWAS_BIN}/
eigstratloc ${XWAS_BIN}/
excludexchrPCA	YES
build 19
alpha 0.05
plinkformat bed
exclind 0
maf 0.005
missindiv 0.1
missgeno 0.1
numpc 10
related 0.125
quant 0
END_OF_CONFIG
[user@cn3144]$ xwas_qc.post_imputation.sh qc.par

Next, an example of how to do some association tests

[user@cn3144]$ cp -r ${XWAS_TEST_DATA} .
[user@cn3144]$ cd example/gene_test
[user@cn3144]$ cat > example_params_gene_test.txt <<END_OF_CONFIG
filename	example_gene_test
xwasloc	${XWAS_BIN}/
genescriptloc	${XWAS_BIN}/
genelistname	example_gene_test_list.txt
assocfile	example_gene_test_snp_pval.txt
numindiv 50
buffer	15000
output	example_gene_test_result.txt
END_OF_CONFIG

[user@cn3144]$ gene_based_test.sh example_params_gene_test.txt
[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf]$

xwas allows many different analyses. Please see the manual for more documentation.

Create a batch input file (e.g. xwas.sh), which uses the input file 'xwas.in'. For example:

#! /bin/bash
# this file is impute.sh

# create required directories
mkdir -p example_X_final example_X_step1 example_X_step2

# create a parameter file
cat > example.par <<END_OF_CONFIG
FILE: hapmap3_euro_all
OUTPUT: hapmap3_chr23_imputed
NJOBS: 31
BUILD: 18
FILELOC: example_X_loc/
REFLOC: ${XWAS_DB}/impute_ref/
TOOLSLOC: ${XWAS_IMPUTE_BIN}/
RESLOC1: example_X_step1/
RESLOC2: example_X_step2/
FINALRESLOC: example_X_final/
MAFRULE: EUR.MAF<=0.005
END_OF_CONFIG

# create all the scripts
make_imputation_files example.par

par="--time=60 --partition=quick"
# run step 1
jid1=$(sbatch --mem=2g ${par} hapmap3_euro_all_preimpute.sh)
[[ $? -eq 0 ]] || exit 1
echo "Submitted step 1: ${jid1}"

# run step 2
jid2=$(swarm -t1 -p2 -g2 ${par} --dependency=afterany:${jid1} -f hapmap3_euro_all_impute2_run_all.sh)
[[ $? -eq 0 ]] || exit 1
echo "Submitted step 2: ${jid2}"

# run step 3
jid3=$(sbatch --dependency=afterany:${jid2} ${par} --mail-type=ALL --mem=6g hapmap3_euro_all_impute2_cat.sh)
[[ $? -eq 0 ]] || exit 1
echo "Submitted step 3: ${jid3}"

sleep 5s
squeue -j ${jid1},${jid2},${jid3}

Submit this job using the Slurm sbatch command.

sbatch xwas.sh