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VQSR_MAIN_SLURM_JUN2018.sh
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VQSR_MAIN_SLURM_JUN2018.sh
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#!/bin/bash
./VQSR_1_SLURM.sh $1
JOBID0=$(sbatch VQSR_1_STEP.sh)
if ! echo ${JOBID0} | grep -q "[1-9][0-9]*$"; then
echo "Job(s) submission failed."
echo ${JOBID0}
exit 1
else
job0=$(echo ${JOBID0} | grep -oh "[1-9][0-9]*$")
fi
echo " SNP RECALIBRATION COMPELTED NOW APPLYING RECALIBRATION MAKE SURE TO CHECK THE RSCRIPTS TO GENERATE PLOTS"
./VQSR_2_SLURM.sh $job0 $1
JOBID1=$(sbatch VQSR_2_STEP.sh)
if ! echo ${JOBID1} | grep -q "[1-9][0-9]*$"; then
echo "Job(s) submission failed."
echo ${JOBID1}
exit 1
else
job1=$(echo ${JOBID1} | grep -oh "[1-9][0-9]*$")
fi
echo "VQSR of SNPS in progress "
./VQSR_3_SLURM.sh $job1 $1
JOBID2=$(sbatch VQSR_3_STEP.sh)
if ! echo ${JOBID2} | grep -q "[1-9][0-9]*$"; then
echo "Job(s) submission failed."
echo ${JOBID2}
exit 1
else
job2=$(echo ${JOBID2} | grep -oh "[1-9][0-9]*$")
fi
echo "VQSR of INDELS in progress "
echo "VQSR of INDELS finshed "
./VQSR_4_SLURM.sh $job2 $1
sbatch VQSR_4_STEP.sh