Newer
Older
#!/bin/bash
#PBS -l walltime=02:00:00
#PBS -l ncpus=1,mem=16gb
#PBS -N cov_wes_pilot
#PBS -j oe
not finished
# enable running singletons
if [ -z $PBS_ARRAY_INDEX ]
then
if [ -z $INDEX ]
then
export PBS_ARRAY_INDEX=1
else
export PBS_ARRAY_INDEX=$INDEX
fi
fi
export PATH=$PATH:/home/u035/u035/shared/software/bcbio-1.1.3/tools/bin
BCBIO_CONFIG=/scratch/u035/u035/shared/analysis/wes_pilot/bcbio/config
BCBIO_WORK=/scratch/u035/u035/shared/analysis/wes_pilot/bcbio/work
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
# Expects environment variables to be set
# BATCH - date yyyymmdd batch
# FAMILY_IDS - text file listing family ids
FAMILY_ID=`head -n $PBS_ARRAY_INDEX $FAMILY_IDS | tail -n 1`
CONFIG_FILE=$BCBIO_CONFIG/${BATCH}_${FAMILY_ID}_prepare_samples-merged.yaml
mkdir -p $BCBIO_WORK/$FAMILY_ID
cd $BCBIO_WORK/$FAMILY_ID
bcbio_nextgen.py $CONFIG_FILE -n 16 -t local
//////////////////////////////////////////
#!/bin/bash
# To run this script, do
# qsub -t 1-n submit_depth_of_coverage.sh IDS TARGETS BCBIO_UPLOAD_DIR COVERAGE_DIR
#
#$ -N coverage
#$ -j y
#$ -S /bin/bash
#$ -cwd
#$ -l h_rt=01:00:00
#$ -l h_vmem=16G
unset MODULEPATH
. /etc/profile.d/modules.sh
module load java/jdk/1.8.0
PARAMS=$1
TARGETS=$2
BCBIO_UPLOAD_DIR=$3
COVERAGE_DIR=$4
ID=`head -n $SGE_TASK_ID $PARAMS | tail -n 1`
export GATK3=/exports/igmm/eddie/NextGenResources/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
export REF=/exports/igmm/eddie/bioinfsvice/ameynert/software/bcbio-1.0.6/genomes/Hsapiens/hg38/seq/hg38.fa
BAM=$BCBIO_UPLOAD_DIR/$ID/$ID/$ID-ready.bam
OUT=$COVERAGE_DIR/$ID
java -Xmx4g -jar $GATK3 -T DepthOfCoverage -R $REF -o $OUT -I $BAM -L $TARGETS \
--omitDepthOutputAtEachBase \
--minBaseQuality 20 \
--minMappingQuality 20 \
-ct 1 -ct 5 -ct 10 -ct 15 -ct 20 -ct 25 -ct 30 -ct 50 \
--allow_potentially_misencoded_quality_scores