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Copy pathCNVnator_0.bash
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CNVnator_0.bash
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#!/bin/bash
# Example usage:
# INDIR=/data/neurogenetics/alignments/Illumina/genomes/CPtwins OUTDIR=/fast/users/a1742674/outputs/SVcalling/cnvnatorOut sbatch --array 0-159 cnvnatorCall.sh
#SBATCH -A robinson
#SBATCH -p batch
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --time=10:00:00
#SBATCH --mem=32GB
# Notification configuration
#SBATCH --mail-type=END
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=%[email protected]
# directories
CHROMDIR=/data/neurogenetics/RefSeq/chromosomes_hs37d5
INDIR=/data/neurogenetics/alignments/Illumina/genomes/CPtwins
OUTDIR=/fast/users/a1742674/outputs/SVcalling/cnvnator
# define query bam files
QUERIES=($(ls $INDIR/*.bam | xargs -n 1 basename))
# load modules
# module load ROOT/v5.34.09-foss-2015b
module load ROOT/v6.09.02-foss-2016b-Python-2.7.13
module load GCC/4.9.3-binutils-2.25
# module load CNVnator/0.3.2-GCC-4.9.3-binutils-2.25
module load CNVnator/0.3.3-foss-2016b
# run the thing
### CNV discovery/calling phase ###
echo $(date +"[%b %d %H:%M:%S] Starting cnvnator")
echo "Processing file: "${QUERIES[$SLURM_ARRAY_TASK_ID]}
echo $(date +"[%b %d %H:%M:%S] Extracting read mapping from BAM files...")
cnvnator -root ${QUERIES[$SLURM_ARRAY_TASK_ID]}.root \
-tree ${INDIR}/${QUERIES[$SLURM_ARRAY_TASK_ID]}
echo $(date +"[%b %d %H:%M:%S] Generating a histogram...")
cnvnator -root ${QUERIES[$SLURM_ARRAY_TASK_ID]}.root \
-his 100 -d $CHROMDIR
echo $(date +"[%b %d %H:%M:%S] Calculating stats...")
cnvnator -root ${QUERIES[$SLURM_ARRAY_TASK_ID]}.root \
-stat 100
echo $(date +"[%b %d %H:%M:%S] Partitioning...")cd .
cnvnator -root ${QUERIES[$SLURM_ARRAY_TASK_ID]}.root \
-partition 100
echo $(date +"[%b %d %H:%M:%S] Calling CNVs...")
cnvnator -root ${QUERIES[$SLURM_ARRAY_TASK_ID]}.root \
-call 100 \
-f ${INDIR}/${QUERIES[$SLURM_ARRAY_TASK_ID]} \
> ${OUTDIR}/${QUERIES[$SLURM_ARRAY_TASK_ID]}.out \
2> ${OUTDIR}/${QUERIES[$SLURM_ARRAY_TASK_ID]}.log
echo $(date +"[%b %d %H:%M:%S] Converting to VCF format...")
cnvnator2VCF.pl ${OUTDIR}/${QUERIES[$SLURM_ARRAY_TASK_ID]}.out $CHROMDIR \
> ${OUTDIR}/${QUERIES[$SLURM_ARRAY_TASK_ID]}.vcf
echo $(date +"[%b %d %H:%M:%S] All done!")