Newer
Older
#!/bin/bash
#PBS -l walltime=24:00:00
#PBS -l ncpus=1,mem=16gb
#PBS -q uv2000
#PBS -N process_trio
#PBS -j oe
# setup PATH
export PATH=$PATH:/home/u035/project/software/bcbio/anaconda/envs/python2/bin:/home/u035/project/software/bcbio/anaconda/bin
export PERL5LIB=$PERL5LIB:/home/u035/project/software/bcbio/anaconda/lib/site_perl/5.26.2
### folder structure for the downstream analysis - created by NHS_WES_trio_setup.sh ###
WORK_DIR=$BASE/${PROJECT_ID}
VCF_DIR=${WORK_DIR}/VCF
PED_DIR=${WORK_DIR}/PED
LOG_DIR=${WORK_DIR}/LOG
G2P_DIR=${WORK_DIR}/G2P
VASE_DIR=${WORK_DIR}/VASE
COV_DIR=${WORK_DIR}/COV
DEC_DIR=${WORK_DIR}/DECIPHER
IGV_DIR=${DEC_DIR}/IGV
CNV_DIR=${WORK_DIR}/CNV
# other files to be used
FAMILY_IDS=${WORK_DIR}/FAM_IDs.txt # created by NHS_WES_trio_setup.sh
CHILD_IDS=${WORK_DIR}/PRO_IDs.txt # created by NHS_WES_trio_setup.sh
TARGETS=/home/u035/project/resources/DDG2P.20190919.plus15bp.merged.bed # OK
CLINVAR=/home/u035/project/resources/DDG2P.20190919.clinvar.20190916.plus15bp.txt # OK
BLACKLIST=/home/u035/project/resources/current_blacklist.txt # OK
TRANS_MAP=/home/u035/project/resources/current_trans_map.txt # OK
BCFTOOLS=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bcftools
BGZIP=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bgzip
TABIX=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/tabix
VT=/home/u035/project/software/bcbio/anaconda/bin/vt
VASE=/home/u035/project/software/bcbio/anaconda/bin/vase
GATK4=/home/u035/project/software/bcbio/anaconda/bin/gatk
GATK3=/home/u035/project/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
PYTHON2=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/python2.7
VEP="/home/u035/project/software/bcbio/anaconda/bin/perl /home/u035/project/software/bcbio/anaconda/bin/vep" # points to ../share/ensembl-vep-97.3-0/vep
REFERENCE_GENOME=/home/u035/project/data/reference/hg38.fa
echo "SOURCE_DIR = ${SOURCE_DIR}" # the general path to the source BAM files (VCF and PED already copied) i.e. /scratch/u035/project/trio_whole_exome/analysis/output/
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
echo "BATCH_ID = ${BATCH_ID}" # the ID of the batch being processed e.g. 11870_Germain_Lorna
echo "PLATE_ID = ${PLATE_ID}" # the PCR plate ID of the batch being currently processed, e.g. 16862
echo "PROJECT_ID = ${PROJECT_ID}" # this the the folder (${BASE}/${PROJECT_ID}) where the downstream analysis will be done
# 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
# change to the LOG folder
cd ${LOG_DIR}
################################
##### for each family ####
################################
FAMILY_ID=`head -n ${PBS_ARRAY_INDEX} ${FAMILY_IDS} | tail -n 1`
###################################################################################
### for each proband generate the DECIPHER file ###
### ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}.ready.vcf.gz - the cleaned family VCF ###
### ${VASE_DIR}/${PLATE_ID}_${FAMILY_ID}.ready.denovo.vcf - the VASE file ###
### ${TRANS_MAP} - the current transcript mapping file ###
###################################################################################
echo "Generating the DECIPHER file for PROBAND_ID = ${PROBAND_ID}_${FAMILY_ID} ..."
# # first, split the family VCF to individual VCFs
# # -c1: minimum allele count (INFO/AC) of sites to be printed
# # split multi-allelic sites (by -m -any)
# # left-alignment and normalization (by adding the -f)
# file=${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}.ready.vcf.gz
# echo "splitting $file"
# for indi in `${BCFTOOLS} query -l $file`; do
# ${BCFTOOLS} view -c1 -Oz -s $indi -o ${file/.vcf*/.$indi.rough.vcf.gz} $file
# ${BCFTOOLS} norm -f ${REFERENCE_GENOME} -m -any -Oz -o ${file/.vcf*/.$indi.vcf.gz} ${file/.vcf*/.$indi.rough.vcf.gz}
# rm ${file/.vcf*/.$indi.rough.vcf.gz}
# done
# # VASE file - already split, left-aligned and normalized
# create the names of the needed files
PED_FILE=${PED_DIR}/${BATCH_ID}_${PLATE_ID}_${FAMILY_ID}.ped
DEC_MAP=${WORK_DIR}/DECIPHER_INTERNAL_IDs.txt
IN_G2P_FILE=${G2P_DIR}/${PLATE_ID}_${FAMILY_ID}_LOG_DIR/${PLATE_ID}_${FAMILY_ID}.report.txt
IN_VASE_FILE=${VASE_DIR}/${PLATE_ID}_${FAMILY_ID}.ready.denovo.vcf
FAM_IGV_DIR=${IGV_DIR}/${PLATE_ID}_${FAMILY_ID}
FAM_BAM_DIR=${SOURCE_DIR}/????-??-??_${BATCH_ID}_${PLATE_ID}_${FAMILY_ID}
## call the python scrpit
time ${PYTHON2} ${SCRIPTS_DIR}/NHS_WES_generate_DEC_IGV.py \
${DEC_MAP} \
${TRANS_MAP} \
${PED_FILE} \
${IN_G2P_FILE} \
${IN_VASE_FILE} \
${FAM_IGV_DIR} \
${VCF_DIR} \
${PLATE_ID} \
${FAMILY_ID} \
${DEC_DIR} \
${FAM_BAM_DIR}
echo ""
echo ""
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo "DECIPHER analysis of PROBAND_ID = ${PROBAND_ID}_${FAMILY_ID}: done"
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo ""
echo ""