-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathsv_pipe_hardcode_37.sh
163 lines (131 loc) · 5.51 KB
/
sv_pipe_hardcode_37.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
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
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
#!/bin/bash
#SBATCH --job-name=sv_pipeline
#SBATCH --time=14:00:00
#SBATCH --account=marth-rw
#SBATCH --partition=marth-rw
#SBATCH -o ./slurm-%j.out-%N
#SBATCH -e ./slurm-%j.err-%N
#SBATCH --nodes=1
#SBATCH --mail-type=ALL
#SBATCH --mail-user=<your_email>
#Inputs to the script
YMLDEF=$1
# Grab the neccessary items from the YMLDEF passed via the command
CRAMSPATH=$(grep 'cramsPath:' "$YMLDEF" | awk '{print $2}')
PROBANDID=$(grep 'probandId:' "$YMLDEF" | awk '{print $2}')
PARENT1ID=$(grep 'parent1Id:' "$YMLDEF" | awk '{print $2}')
PARENT2ID=$(grep 'parent2Id:' "$YMLDEF" | awk '{print $2}')
O_SMOOVE_VCF=$(grep 'smoove:' "$YMLDEF" | awk '{print $2}')
REF_FASTA='human_g1k_v37_decoy_phix.fasta'
FASTA_FOLDER='/scratch/ucgd/lustre-core/common/data/Reference/GRCh37'
DOCTORED_MANTA_OUTPUT="doctor_manta.vcf.gz"
DUPHOLD_MANTA_OUTPUT="duphold_manta.vcf.gz"
SVAF_SMOOVE_OUTPUT="svaf_smoove.vcf"
SVAF_MANTA_OUTPUT="svaf_manta.vcf"
DMANTAFILE="filtered_manta.vcf.gz"
DSMOOVEFILE="filtered_smoove.vcf.gz"
# Set up scratch directory
FOLDERNAME=${PROBANDID}_${SLURM_JOB_ID}
SCRDIR=./$FOLDERNAME
mkdir $SCRDIR
cd $SCRDIR
# Copy the scripts and reference files to the scratch dir
cp \
/scratch/ucgd/lustre-labs/marth/scratch/u1069837/data/sv_pipeline_work/run_manta_trio_37.sh \
/scratch/ucgd/lustre-labs/marth/scratch/u1069837/data/sv_pipeline_work/doctor_manta.py \
/scratch/ucgd/lustre-labs/marth/scratch/u1069837/data/sv_pipeline_work/smoove/bp_smoove.sif \
/scratch/ucgd/lustre-labs/marth/scratch/u1069837/data/sv_pipeline_work/sv_pipe.yml \
/scratch/ucgd/lustre-labs/marth/scratch/u1069837/data/sv_pipeline_work/ref_files/SVAFotate_core_SV_popAFs.GRCh37.v4.1.bed.gz \
.
mkdir "duphold_run"
# Run the the manta script run_manta_trio.sh (needs the trio's urls CRAM format) -> new joint called vcf
echo "run manta trio"
./run_manta_trio.sh $CRAMSPATH/$PROBANDID.cram $CRAMSPATH/$PARENT1ID.cram $CRAMSPATH/$PARENT2ID.cram
echo "manta complete"
# Load the miniconda3 module will be needed for the doctor_manta.py and for the svafotate run
module load \
miniconda3/23.11.0 \
singularity/4.1.1 \
bcftools/1.16
# Check if the environment already exists, if not create it from the yml
ENV_NAME="sv_pipe_conda_env"
if conda info --envs | grep -q "$ENV_NAME"; then
conda activate "$ENV_NAME"
else
conda env create -f sv_pipe.yml
conda activate "$ENV_NAME"
conda install --file https://raw.githubusercontent.com/fakedrtom/SVAFotate/master/requirements.txt
pip install git+https://github.com/fakedrtom/SVAFotate.git
fi
# Modify the manta vcf (./diploidSV.vcf.gz) with his doctor_manta.py (needs input vcf, and output) -> new doc_vcf
python doctor_manta.py diploidSV.vcf.gz $DOCTORED_MANTA_OUTPUT
BIND_DIR=$(pwd -P)
cp $DOCTORED_MANTA_OUTPUT ./duphold_run/$DOCTORED_MANTA_OUTPUT
# Run smoove duphold on the manta vcf -> dhanno_manta_vcf
echo "Run Duphold"
singularity exec \
--bind $BIND_DIR/duphold_run:/output \
--bind $CRAMSPATH:/crams \
--bind $FASTA_FOLDER:/fastas \
bp_smoove.sif \
smoove duphold \
-f /fastas/$REF_FASTA \
-v /output/$DOCTORED_MANTA_OUTPUT \
-o /output/$DUPHOLD_MANTA_OUTPUT \
/crams/$PROBANDID.cram /crams/$PARENT1ID.cram /crams/$PARENT2ID.cram
echo "duphold complete"
# Move the duphold output to the main folder for use in svafotate
mv ./duphold_run/$DUPHOLD_MANTA_OUTPUT ./$DUPHOLD_MANTA_OUTPUT
# Run svafotate on both files (.8 ol threshold) -> filtered svaf_vcf
#TODO: Change both references to the 37 version
echo "Run svafotate on MANTA"
svafotate annotate -v ./$DUPHOLD_MANTA_OUTPUT -b SVAFotate_core_SV_popAFs.GRCh37.v4.1.bed.gz -o $SVAF_MANTA_OUTPUT -f 0.8 --cpu 12
bgzip $SVAF_MANTA_OUTPUT
echo "manta svafotate complete"
echo "running svafotate on smoove"
svafotate annotate -v $O_SMOOVE_VCF -b SVAFotate_core_SV_popAFs.GRCh37.v4.1.bed.gz -o $SVAF_SMOOVE_OUTPUT -f 0.8 --cpu 12
bgzip $SVAF_SMOOVE_OUTPUT
echo "smoove svafotate complete"
conda deactivate
# Load sample names from the VCF file into the SAMPLES array
SAMPLES=($(bcftools query -l "$SVAF_SMOOVE_OUTPUT.gz"))
PROB_INDEX=-1
# Find the index of the proband sample in the SAMPLES array
for i in "${!SAMPLES[@]}"; do
if [[ "${SAMPLES[$i]}" == "$PROBANDID" ]]; then
PROB_INDEX=$i
break
fi
done
# Check if the proband index was found
if [[ "$PROB_INDEX" -lt 0 ]]; then
echo "Error: Proband sample not found in VCF file."
exit 1
fi
# Construct the bcftools command using the dynamically determined indices
bcftools view -i '((INFO/SVTYPE="DEL" && FMT/DHFFC['"$PROB_INDEX"']<0.7) || \
(INFO/SVTYPE="DUP" && FMT/DHBFC['"$PROB_INDEX"']>1.3) || \
(INFO/SVTYPE!="DEL" && INFO/SVTYPE!="DUP")) && \
INFO/Max_AF<0.05' "$SVAF_SMOOVE_OUTPUT.gz" -Oz -o "$DSMOOVEFILE"
# Construct the bcftools command using the dynamically determined indices
bcftools view -i '((INFO/SVTYPE="DEL" && FMT/DHFFC['"$PROB_INDEX"']<0.7) || \
(INFO/SVTYPE="DUP" && FMT/DHBFC['"$PROB_INDEX"']>1.3) || \
(INFO/SVTYPE!="DEL" && INFO/SVTYPE!="DUP")) && \
INFO/Max_AF<0.05' "$SVAF_MANTA_OUTPUT.gz" -Oz -o "$DMANTAFILE"
# Cleanup
rm run_manta_trio.sh \
runWorkflow.py \
runWorkflow.py.config.pickle \
diploidSV.vcf.gz \
doctor_manta.py \
doctor_manta.vcf.gz \
duphold_manta.vcf.gz \
bp_smoove.sif \
sv_pipe.yml \
SVAFotate_core_SV_popAFs.GRCh37.v4.1.bed.gz \
workflow.error.log.txt \
workflow.exitcode.txt \
workflow.warning.log.txt
rm -r ./duphold_run
rm -r ./results
rm -r ./workspace