genotypegVCFs

#!/bin/bash
# This options tells gridware to change to the current directory before
# executing the job (default is the home of the user)
#$-cwd
#
# This option declares the amount of memory the job will
# use. Specify this value as accurat as possible. If you
# declare too low memory usage, your job may be aborted.
# If you declare too high memory usage, your job might be
# wait for a long time until it is started on a machine
# that has the sufficient amount of free memory.
#$-l vf=10G
#
# Specify this option only for multithreaded jobs that use
# more than one cpu core. The value 1..24 denotes the number
# of requested cpu cores. Please note that multithreaded jobs
# are always calculated on a single machine - for parallel
# jobs you should use MPI instead.
# Another important hint: memory request by -l vf=... are
# multiplied by the number of requested cpu cores. Thus you
# should divide the overall memory consumption of your job by
# the number of parallel threads.
#$-pe serial 1
#$-q bigmem
#
# -- Job name ---
#$ -N GenotypeGVCFs
#$ -S /bin/bash
#
# Please insert your mail address!
#$-M kai.wei@tum.de

export LD_LIBRARY_PATH=/cluster/java/latest/jre/lib/amd64:/cluster/java/latest/jre/lib/amd64/server:/cluster/java/latest/jre/lib/amd64/xawt:/cluster/java/latest/lib:/cluster/boost-1_64_0/lib:/cluster/gsl-2.3/lib
export PATH=/cluster/gridengine/ge2011.11/bin/linux-x64:/cluster/openmpi/bin:/cluster/java/latest/bin:/cluster/software/bin:/sysinst/bin:/cluster/gridengine/ge2011.11/bin/linux-x64:/usr/lib64/qt-3.3/bin:/cluster/openmpi/bin:/cluster/java/latest/bin:/cluster/software/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin:/data/proj/teaching/NGS_course/bin/

ref="/data/proj/chilense/30_genomes_outputs/kai_wei/variant_call/CNVs/spenn_Assem_GCA_001406875.2/spenn.fasta"
GATK="java -jar /data/proj/teaching/NGS_course/Softwares/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar"

# mkdir /localscratch/GenotypeGVCFs
# mkdir /localscratch/GenotypeGVCFs/output

 $GATK -R $ref -T GenotypeGVCFs \
   --variant 31genomes.GATK.g.vcf \
   -o 31genomes.GATK.raw.vcf.gz 

# mv /localscratch/GenotypeGVCFs/output /data/proj/chilense/30_genomes_outputs/kai_wei/variant_call/new_calling
# rm -rf /localscratch/GenotypeGVCFs