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shapeit_phasing_job.sh
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shapeit_phasing_job.sh
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## Prephasing each CHR using SHAPEIT . The following example is for CHR1, replace the CHR number to do Prephasing on each CHR
#!/bin/bash
#PBS -W group_list=#### -A ####
#PBS -N prephasing_shapeit
#PBS -o $PBS_JOBID.out
#PBS -e $PBS_JOBID.err
#PBS -l nodes=1:ppn=10
#PBS -l walltime=99:00:00
module load shapeit/2.r837
cd /home/projects/####/data/1000_genome/
CHR=1
# directories
ROOT_DIR=./
DATA_DIR=${ROOT_DIR}data_files/
RESULTS_DIR=${ROOT_DIR}results/
# executable
#SHAPEIT_EXEC=${ROOT_DIR}shapeit
# parameters
THREAT=4
EFFECTIVESIZE=11418
# reference data files
GENMAP_FILE=${DATA_DIR}genetic_map_chr${CHR}_combined_b37.txt
# GWAS data files in PLINK BED format
GWASDATA_BED=${DATA_DIR}gwas_data_chr${CHR}.bed
GWASDATA_BIM=${DATA_DIR}gwas_data_chr${CHR}.bim
GWASDATA_FAM=${DATA_DIR}gwas_data_chr${CHR}.fam
# main output file
OUTPUT_HAPS=${RESULTS_DIR}chr${CHR}.haps
OUTPUT_SAMPLE=${RESULTS_DIR}chr${CHR}.sample
OUTPUT_LOG=${RESULTS_DIR}chr${CHR}.log
## phase GWAS genotypes
shapeit \
--input-bed $GWASDATA_BED $GWASDATA_BIM $GWASDATA_FAM \
--input-map $GENMAP_FILE \
--thread $THREAT \
--effective-size $EFFECTIVESIZE \
--output-max $OUTPUT_HAPS $OUTPUT_SAMPLE \
--output-log $OUTPUT_LOG