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3_generate_downsample_pileup.sh
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source /autofs/bal36/jhsu/trio/script/data_config_trio.sh
PARALLEL=parallel
PYPY=pypy
SAMTOOLS=samtools
PYTHON3=python3
PLATFORM="ont"
# Clair3 folder
_ORI_CLAIR3="/autofs/bal36/jhsu/trio/Clair3-Nova"
# note the use right models for your training
# check https://github.com/HKU-BAL/Clair3#pre-trained-models
#_MODEL_DIR="/autofs/bal31/jhsu/home/data/clair3_models/r941_prom_sup_g5014/"
_MODEL_DIR="/autofs/bal36/jhsu/trio/models/rerio/clair3_models/r1041_e82_400bps_hac_v430/"
C3_THREADS=36 # Clair3 threads number
# Clair3-Trio's path
CLAIR3_TRIO="/autofs/bal36/jhsu/trio/Clair3-Nova_dev/clair3.py"
DATASET_FOLDER_PATH="/autofs/bal36/jhsu/trio/r1041_hac"
# creating working folder
PILEUP_OUTPUT_PATH="${DATASET_FOLDER_PATH}/3_pileup"
LOG_PATH="${PILEUP_OUTPUT_PATH}"
mkdir -p ${PILEUP_OUTPUT_PATH}
cd ${PILEUP_OUTPUT_PATH}
# input files and parameters
# training chrosome name, and prefix
CHR=(1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 21 22)
CHR_PREFIX="chr"
# GH (tb update to github)
CHILD_SAMPLE_N="HG002"
P1_SAMPLE_N="HG003"
P2_SAMPLE_N="HG004"
# sample name
ALL_SAMPLE=(
${CHILD_SAMPLE_N}
${P1_SAMPLE_N}
${P2_SAMPLE_N}
${CHILD_SAMPLE_N}
${P1_SAMPLE_N}
${P2_SAMPLE_N}
${CHILD_SAMPLE_N}
${P1_SAMPLE_N}
${P2_SAMPLE_N}
${CHILD_SAMPLE_N}
${P1_SAMPLE_N}
${P2_SAMPLE_N}
)
DEPTHS=( # data coverage
10
10
10
30
30
30
60
60
60
80
80
80
)
ALL_PHASED_BAM_FILE_PATH=(
"/autofs/bal36/jhsu/trio/r1041_hac/2_bam/HG002/HG002_10.bam"
"/autofs/bal36/jhsu/trio/r1041_hac/2_bam/HG003/HG003_10.bam"
"/autofs/bal36/jhsu/trio/r1041_hac/2_bam/HG004/HG004_10.bam"
"/autofs/bal36/jhsu/trio/r1041_hac/2_bam/HG002/HG002_30.bam"
"/autofs/bal36/jhsu/trio/r1041_hac/2_bam/HG003/HG003_30.bam"
"/autofs/bal36/jhsu/trio/r1041_hac/2_bam/HG004/HG004_30.bam"
"/autofs/bal36/jhsu/trio/r1041_hac/2_bam/HG002/HG002_60.bam"
"/autofs/bal36/jhsu/trio/r1041_hac/2_bam/HG003/HG003_60.bam"
"/autofs/bal36/jhsu/trio/r1041_hac/2_bam/HG004/HG004_60.bam"
"/autofs/bal36/jhsu/trio/r1041_hac/2_bam/HG002/HG002_80.bam"
"/autofs/bal36/jhsu/trio/r1041_hac/2_bam/HG003/HG003_80.bam"
"/autofs/bal36/jhsu/trio/r1041_hac/2_bam/HG004/HG004_80.bam"
)
#HOME_DIR="/autofs/bal31/jhsu/home"
#REF_FILE_PATH="${HOME_DIR}/data/reference/grch38_no_alt_plus_hs38d1/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna"
#CHILD_BED_FILE_PATH="${HOME_DIR}/data/giab/${CHILD_SAMPLE_N}_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed"
#P1_BED_FILE_PATH="${HOME_DIR}/data/giab/${P1_SAMPLE_N}_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed"
#P2_BED_FILE_PATH="${HOME_DIR}/data/giab/${P2_SAMPLE_N}_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed"
# GH
# merge trio's bed file using the gerneate_trio_bed.sh
#_TRIO_BED_PATH="${HOME_DIR}/data/giab/020304.bed"
ALL_REFERENCE_FILE_PATH=(
"${REF_FILE_PATH}"
"${REF_FILE_PATH}"
"${REF_FILE_PATH}"
"${REF_FILE_PATH}"
"${REF_FILE_PATH}"
"${REF_FILE_PATH}"
"${REF_FILE_PATH}"
"${REF_FILE_PATH}"
"${REF_FILE_PATH}"
"${REF_FILE_PATH}"
"${REF_FILE_PATH}"
"${REF_FILE_PATH}"
)
ALL_BED_FILE_PATH=(
${_TRIO_BED_PATH}
${_TRIO_BED_PATH}
${_TRIO_BED_PATH}
${_TRIO_BED_PATH}
${_TRIO_BED_PATH}
${_TRIO_BED_PATH}
${_TRIO_BED_PATH}
${_TRIO_BED_PATH}
${_TRIO_BED_PATH}
${_TRIO_BED_PATH}
${_TRIO_BED_PATH}
${_TRIO_BED_PATH}
)
# log file suffix name
_LOG_SUF="" # log file suffix
# Run Clair3 pileup model
time ${PARALLEL} -j ${C3_THREADS} --joblog ${LOG_PATH}/input_pileup${_LOG_SUF}.log ${_ORI_CLAIR3}/run_clair3.sh \
--bam_fn={5} \
--ref_fn={2} \
--threads=${C3_THREADS} \
--platform="ont" \
--model_path="${_MODEL_DIR}" \
--output=${PILEUP_OUTPUT_PATH}/{1}_{4} \
--bed_fn={3} \
--pileup_only ::: ${ALL_SAMPLE[@]} :::+ ${ALL_REFERENCE_FILE_PATH[@]} :::+ ${ALL_BED_FILE_PATH[@]} :::+ ${DEPTHS[@]} :::+ ${ALL_PHASED_BAM_FILE_PATH[@]}