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#!/bin/bash
#SBATCH --cpus-per-task=1
#SBATCH --mem=16GB
#SBATCH --time=24:00:00
#SBATCH --job-name=process_quad
#SBATCH --output=process_quad.%A_%a.out
#SBATCH --error=process_quad.%A_%a.err
# setup PATH
export PATH=$PATH:/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin:/home/u035/u035/shared/software/bcbio/anaconda/bin
export PERL5LIB=$PERL5LIB:/home/u035/u035/shared/software/bcbio/anaconda/lib/site_perl/5.26.2
### folder structure for the downstream analysis - created by trio_setup.sh, done previously by the stanard trio-based pipeline ###
BASE=/home/u035/u035/shared/analysis/work
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=${WORK_DIR}/CNV
BAMOUT_DIR=${WORK_DIR}/BAMOUT
SCRIPTS_DIR=/home/u035/u035/shared/scripts
# other files to be used
TARGETS=/home/u035/u035/shared/resources/G2P/DDG2P.20210706.plus15bp.merged.bed # OK
CLINVAR=/home/u035/u035/shared/resources/G2P/DDG2P.20210706.clinvar.20210626.plus15bp.txt # OK
BLACKLIST=/home/u035/u035/shared/resources/blacklist/current_blacklist.txt # OK
TRANS_MAP=/home/u035/u035/shared/resources/trans_map/current_trans_map.txt # OK
### TOOLS ###
BCFTOOLS=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bcftools
BGZIP=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bgzip
TABIX=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/tabix
VT=/home/u035/u035/shared/software/bcbio/anaconda/bin/vt
VASE=/home/u035/u035/shared/software/bcbio/anaconda/bin/vase
GATK4=/home/u035/u035/shared/software/bcbio/anaconda/bin/gatk # points to ../share/gatk4-4.2.1.0-0/gatk
GATK3=/home/u035/u035/shared/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
PYTHON3=/home/u035/u035/shared/software/bcbio/anaconda/bin/python3 # points to python3.6
PYTHON2=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/python2.7
VEP="/home/u035/u035/shared/software/bcbio/anaconda/bin/perl /home/u035/u035/shared/software/bcbio/anaconda/bin/vep" # points to ../share/ensembl-vep-100.4-0/vep
REFERENCE_GENOME=/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
echo "SOURCE_DIR = ${SOURCE_DIR}" # the general path to the source BAM files (VCF and PED already copied) i.e. /home/u035/u035/shared/results
echo "BATCH_ID = ${BATCH_ID}" # the ID of the batch being processed e.g. 19650_Ansari_Morad
echo "BATCH_NUM = ${BATCH_NUM}" # the numerical part of the BATCH_ID e.g. 19650
echo "PLATE_ID = ${PLATE_ID}" # the PCR plate ID of the batch being currently processed, e.g. 19285
echo "PROJECT_ID = ${PROJECT_ID}" # this the the folder (${BASE}/${PROJECT_ID}) where the downstream analysis will be done
echo "VERSION_N = ${VERSION_N}" # the version of the alignment and genotyping analysis
echo "FAMILY_ID = ${FAMILY_ID}" # the family ID of this family with affected probands
echo "KID_1_ID = ${KID_1_ID}" # the ID of the first affected proband, in the format INDI_ID
echo "KID_2_ID = ${KID_2_ID}" # the ID of the second affected proband
echo "PAR_1_ID = ${PAR_1_ID}" # the ID of the first unaffected parent, in the format INDI_ID
echo "PAR_2_ID = ${PAR_2_ID}" # the ID of the second unaffected parent
echo "DECIPHER_ID = ${DECIPHER_ID}" # the DECIPHER_ID for this family
# change to the LOG folder
cd ${LOG_DIR}
#########################################################################################################
### check the PED file to make sure exactly 2 affected probands with exactly 2 unaffected parents ###
#########################################################################################################
echo ""
echo ""
echo "checking the ${PED_DIR}/${BATCH_ID}_${PLATE_ID}_${FAMILY_ID}.ped file..."
time ${PYTHON2} ${SCRIPTS_DIR}/check_quad_PED.py ${PED_DIR}/${BATCH_ID}_${PLATE_ID}_${FAMILY_ID}.ped
# check if the PED file checks were successful (python exit code = 0), if not exit the bash script
ret=$?
if [ $ret -ne 0 ]; then
echo "...it appears that the PED file does not corresponds to a quad family !"
echo "ERROR: Aborting the analysis"
exit
fi
echo ""
echo ""
##################################################################################################
##################################################################################################
### split the quad to two trios, one for each child and process as a standard TRIO family ###
##################################################################################################
##################################################################################################
echo ""
echo ""
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "+++ Analysing QUAD family ${FAMILY_ID} as two trios +++"
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo ""
echo ""
# Create an array of kid ids to loop
KID_IDS=()
KID_IDS+=(${KID_1_ID})
KID_IDS+=(${KID_2_ID})
for KID_ID in ${KID_IDS[@]}; do
echo ""
echo "++++++++++++++++++++++++++++++++++++"
echo "processing trio for child = $KID_ID"
echo "++++++++++++++++++++++++++++++++++++"
echo ""
#############################################################
# generate this trio's PED file #
# named: ${BATCH_ID}_${PLATE_ID}_${FAMILY_ID}_${KID_ID}.ped #
#############################################################
quad_ped_file=${BATCH_ID}_${PLATE_ID}_${FAMILY_ID}.ped
time ${PYTHON2} ${SCRIPTS_DIR}/generate_trio_PED_from_quad.py ${PED_DIR} ${quad_ped_file} ${KID_ID} ${PAR_1_ID} ${PAR_2_ID}
#############################################################################
# generate this trio's VCF file #
# named: ${PLATE_ID}_${FAMILY_ID}_${KID_ID}-gatk-haplotype-annotated.vcf.gz #
#############################################################################
quad_vcf_file=${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz
trio_vcf_file=${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}-gatk-haplotype-annotated.vcf.gz
# tabix index the quad file just in case
time ${TABIX} -p vcf ${quad_vcf_file}
# extract a trio VCF for this kid
time java -Xmx24g -jar ${GATK3} -T SelectVariants \
-R ${REFERENCE_GENOME} \
-V ${quad_vcf_file} \
-sn ${KID_ID}_${FAMILY_ID} \
-sn ${PAR_1_ID}_${FAMILY_ID} \
-sn ${PAR_2_ID}_${FAMILY_ID} \
-jdk_deflater \
-jdk_inflater \
-o ${trio_vcf_file} \
-env
##################################################################################
### DNU and clean the the family VCF ###
### format: ${PLATE_ID}_${FAMILY_ID}_${KID_ID}-gatk-haplotype-annotated.vcf.gz ###
##################################################################################
echo ""
echo ""
echo "Performing DNU and cleaning of the ${PLATE_ID}_${FAMILY_ID}_${KID_ID}'s VCF file..."
time ${VT} decompose -s ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}-gatk-haplotype-annotated.vcf.gz -o ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.decomp.vcf.gz
time ${VT} normalize ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.decomp.vcf.gz -r ${REFERENCE_GENOME} -o ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.norm.vcf.gz
time ${VT} uniq ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.norm.vcf.gz -o ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.DNU.vcf.gz
# remove sites with AC=0
time ${BCFTOOLS} view --min-ac=1 --no-update ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.DNU.vcf.gz > ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.AC0.vcf
# reset GT to no-call if num_ALT < num_ALT_THERSH or VAF < VAF_THRESH and GT != 0/0
# exlude variants from the blacklist (matching on chr,pos,ref,alt)
time ${PYTHON2} ${SCRIPTS_DIR}/filter_LQ_GT.py ${BLACKLIST} ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.AC0.vcf ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.clean.vcf
# bgzip and tabix it
time cat ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.clean.vcf | ${BGZIP} > ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.ready.vcf.gz
time ${TABIX} -p vcf ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.ready.vcf.gz
# delete intermediate files - keep them for now for debugging reasons
rm ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}-gatk-haplotype-annotated.vcf.gz
rm ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.decomp.vcf.gz*
rm ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.norm.vcf.gz*
rm ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.DNU.vcf.gz*
rm ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.AC0.vcf
# to avoid bgzip pipe broken annoying, but not problematic message - skip the next step, the file will be used by G2P as IN_FILE and will be deleted last
# rm ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.clean.vcf
echo ""
echo ""
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo "DNU, AC=0, num_ALT & VAF & blacklist cleaning and of the ${PLATE_ID}_${FAMILY_ID}_${KID_ID}'s VCF file: done"
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo ""
echo ""
###################################################################
### run G2P for this trio VCF (DD genes) ###
### format: ${PLATE_ID}_${FAMILY_ID}_${KID_ID}.clean.vcf ###
###################################################################
echo "Performing G2P analysis (DD genes)for FAMILY_ID = ${PLATE_ID}_${FAMILY_ID}_${KID_ID}..."
echo "Using ${TARGETS}"
IN_FILE=${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.clean.vcf
G2P_LOG_DIR=${G2P_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}_LOG_DIR
mkdir ${G2P_LOG_DIR}
TXT_OUT=${G2P_LOG_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.report.txt
HTML_OUT=${G2P_LOG_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.report.html
VCF_KEYS='gnomADe_r2.1.1_GRCh38|gnomADg_r3.1.1_GRCh38'
time ${VEP} \
-i ${IN_FILE} \
--output_file ${G2P_LOG_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}_inter_out.txt \
--force_overwrite \
--assembly GRCh38 \
--fasta ${REFERENCE_GENOME} \
--offline \
--merged \
--use_given_ref \
--cache --cache_version 100 \
--dir_cache /home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/vep \
--individual all \
--transcript_filter "gene_symbol in /home/u035/u035/shared/resources/G2P/genes_in_DDG2P.20210706.txt" \
--dir_plugins /home/u035/u035/shared/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
--plugin G2P,file='/home/u035/u035/shared/resources/G2P/DDG2P.20210706.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
echo ""
echo ""
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo "G2P analysis of FAMILY_ID = ${PLATE_ID}_${FAMILY_ID}_${KID_ID}: done"
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo ""
###################################################################
### run VASE for this trio VCF (de novo) ###
### format: ${PLATE_ID}_${FAMILY_ID}_${KID_ID}.ready.vcf.gz ###
###################################################################
echo "Performing de novo analysis with VASE for FAMILY_ID = ${PLATE_ID}_${FAMILY_ID}_${KID_ID} ..."
IN_FILE=${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.ready.vcf.gz
OUT_FILE=${VASE_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.strict.denovo.vcf
PED_FILE=${PED_DIR}/${BATCH_ID}_${PLATE_ID}_${FAMILY_ID}_${KID_ID}.ped
time ${VASE} \
-i ${IN_FILE} \
-o ${OUT_FILE} \
--log_progress \
--prog_interval 100000 \
--freq 0.0001 \
--gq 30 --dp 10 \
--het_ab 0.3 \
--max_alt_alleles 1 \
--csq all \
--biotypes all \
--control_gq 15 --control_dp 5 \
--control_het_ab 0.01 \
--control_max_ref_ab 0.05 \
--de_novo \
--ped ${PED_FILE}
# do some filtering on the denovo VCFs - exclude variants not on the 24 chr, as well as variants in LCR and telomere/centromere regions
### actually, ignore the filtering of variants in LCR and telomere/centromere regions --> more variants with “Unknown” status may be classified as “denovo” if enough support
cd ${VASE_DIR}
# index the denovo VCF
time ${GATK4} IndexFeatureFile -I ${OUT_FILE}
# select only variants on the 24 chromosomes
time ${GATK4} SelectVariants -R ${REFERENCE_GENOME} -V ${OUT_FILE} -O ${PLATE_ID}_${FAMILY_ID}_${KID_ID}.strict.24chr.denovo.vcf -L /home/u035/u035/shared/resources/24_chr.list --exclude-non-variants
# sort the VCF (maybe not needed?, but just in case, and it is quick)
rm ${PLATE_ID}_${FAMILY_ID}_${KID_ID}.strict.24chr.sort.denovo.vcf
grep '^#' ${PLATE_ID}_${FAMILY_ID}_${KID_ID}.strict.24chr.denovo.vcf > ${PLATE_ID}_${FAMILY_ID}_${KID_ID}.strict.24chr.sort.denovo.vcf \
&& grep -v '^#' ${PLATE_ID}_${FAMILY_ID}_${KID_ID}.strict.24chr.denovo.vcf | LC_ALL=C sort -t $'\t' -k1,1V -k2,2n >> ${PLATE_ID}_${FAMILY_ID}_${KID_ID}.strict.24chr.sort.denovo.vcf
# index the sorted VCF
time ${GATK4} IndexFeatureFile -I ${PLATE_ID}_${FAMILY_ID}_${KID_ID}.strict.24chr.sort.denovo.vcf
# split multi-allelic sites [by -m -any]
# left-alignment and normalization [by adding the -f]
file=${PLATE_ID}_${FAMILY_ID}_${KID_ID}.strict.24chr.sort.denovo.vcf
echo "$file"
${BCFTOOLS} norm -f ${REFERENCE_GENOME} -m -any -Ov -o ${file/.strict.24chr.sort.denovo.vcf/.ready.denovo.vcf} $file
# clean intermediate denovo files
rm ${PLATE_ID}_${FAMILY_ID}_${KID_ID}.strict.denovo.vcf*
rm ${PLATE_ID}_${FAMILY_ID}_${KID_ID}.strict.24chr.denovo.vcf*
rm ${PLATE_ID}_${FAMILY_ID}_${KID_ID}.strict.24chr.sort.denovo.vcf*
# change back to the LOG folder
cd ${LOG_DIR}
echo ""
echo ""
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo "De novo analysis of FAMILY_ID = ${PLATE_ID}_${FAMILY_ID}_${KID_ID}: done"
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo ""
echo ""
#################################################################################################################################################
### run coverage for this proband (DD genes) ###
### format: ${SOURCE_DIR}/????-??-??_${VERSION_N}_${BATCH_ID}_${PLATE_ID}_${FAMILY_ID}/${PROBAND_ID}_${FAMILY_ID}/${PROBAND_ID}_${FAMILY_ID}-ready.bam ###
#################################################################################################################################################
echo "Performing coverage analysis for PROBAND_ID = ${KID_ID} ...."
# make sure we are reading the data from the exact batch & plate ID & version N
BAM_FILE=${SOURCE_DIR}/${BATCH_NUM}_${VERSION_N}/families/????-??-??_${BATCH_NUM}_${VERSION_N}_${PLATE_ID}_${FAMILY_ID}/${KID_ID}_${FAMILY_ID}/${KID_ID}_${FAMILY_ID}-ready.bam
OUT_FILE=${COV_DIR}/${KID_ID}_${FAMILY_ID}.DD15
time java -Xmx8g -jar ${GATK3} -T DepthOfCoverage -R ${REFERENCE_GENOME} -o ${OUT_FILE} -I ${BAM_FILE} -L ${TARGETS} \
--omitDepthOutputAtEachBase \
--minBaseQuality 20 \
--minMappingQuality 20 \
-ct 20 \
-jdk_deflater \
-jdk_inflater \
--allow_potentially_misencoded_quality_scores
echo ""
echo ""
echo "----------------------------------------------------------------------------------------------------"
echo "percentage of DD exons (+/-15bp) covered at least 20x in PROBAND_ID = ${KID_ID} ..."
cat ${COV_DIR}/${KID_ID}_${FAMILY_ID}.DD15.sample_summary | awk '{print $7}'
echo "----------------------------------------------------------------------------------------------------"
# now compute the coverage per DD exon (+/-15bp) interval, adding the number of P/LP ClinVar variants (assertion criteria provided) in each interval
time ${PYTHON2} ${SCRIPTS_DIR}/get_cov_output.py ${COV_DIR}/${KID_ID}_${FAMILY_ID}.DD15.sample_interval_summary ${CLINVAR} ${COV_DIR}/${KID_ID}_${FAMILY_ID}.DD15.COV.txt
echo ""
echo ""
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo "Coverage analysis of PROBAND_ID = ${KID_ID}_${FAMILY_ID}: done "
echo " Coverage file = ${COV_DIR}/${KID_ID}_${FAMILY_ID}.DD15.COV.txt"
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo ""
echo ""
#############################################################################################
### generate the DECIPHER file for this proband ###
### ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.ready.vcf.gz - the cleaned family VCF ###
### ${VASE_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.ready.denovo.vcf - the VASE file ###
### ${TRANS_MAP} - the current transcript mapping file ###
#############################################################################################
echo "Generating the DECIPHER file for PROBAND_ID = ${KID_ID}_${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}_${FAMILY_ID}_${KID_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}_${KID_ID}.ped
IN_G2P_FILE=${G2P_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}_LOG_DIR/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.report.txt
IN_VASE_FILE=${VASE_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.ready.denovo.vcf
FAM_IGV_DIR=${IGV_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}
FAM_BAM_DIR=${SOURCE_DIR}/${BATCH_NUM}_${VERSION_N}/families/????-??-??_${BATCH_NUM}_${VERSION_N}_${PLATE_ID}_${FAMILY_ID}
## call the python scrpit
time ${PYTHON2} ${SCRIPTS_DIR}/generate_DEC_IGV_trio_scripts_from_quad.py \
${DECIPHER_ID} \
${TRANS_MAP} \
${PED_FILE} \
${IN_G2P_FILE} \
${IN_VASE_FILE} \
${FAM_IGV_DIR} \
${VCF_DIR} \
${PLATE_ID} \
${FAMILY_ID} \
${DEC_DIR} \
${FAM_BAM_DIR} \
${KID_ID}
## using the DECIPHER bulk upload file v9 --> generate the DECIPHER bulk upload file v10
echo "...Generating v10 Decipher bulk upload file for proband = ${KID_ID}, family_id = ${FAMILY_ID} ..."
time ${PYTHON3} ${SCRIPTS_DIR}/convert_DEC_to_v10.py ${DEC_DIR} ${KID_ID}_${FAMILY_ID}
echo ""
echo ""
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo "DECIPHER analysis of PROBAND_ID = ${KID_ID}_${FAMILY_ID}: done"
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo ""
echo ""
#rm ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}.clean.vcf
##############################################################################################
### for each variant in the DECIPHER upload file ###
### generate a IGV snapshot based on the realigned BAM used by GATK for calling variants ###
### first, generate BAMOUTs for each variant (to be stored in the BAMOUT folder) ###
### then, generate a batch script for IGV to produce the snapshots based on the BAMOUTs ###
##############################################################################################
# we have so far: FAMILY_ID and KID_ID
echo "...Generating BAMOUT files for the ${FAMILY_ID} family, proband = ${KID_ID} ..."
echo "...KID_ID = ${KID_ID}, PAR_1_ID = ${PAR_1_ID}, PAR_2_ID = ${PAR_2_ID} "
# gather the trio BAM files
kid_bam=${SOURCE_DIR}/${BATCH_NUM}_${VERSION_N}/families/????-??-??_${BATCH_NUM}_${VERSION_N}_${PLATE_ID}_${FAMILY_ID}/${KID_ID}_${FAMILY_ID}/${KID_ID}_${FAMILY_ID}-ready.bam
par_1_bam=${SOURCE_DIR}/${BATCH_NUM}_${VERSION_N}/families/????-??-??_${BATCH_NUM}_${VERSION_N}_${PLATE_ID}_${FAMILY_ID}/${PAR_1_ID}_${FAMILY_ID}/${PAR_1_ID}_${FAMILY_ID}-ready.bam
par_2_bam=${SOURCE_DIR}/${BATCH_NUM}_${VERSION_N}/families/????-??-??_${BATCH_NUM}_${VERSION_N}_${PLATE_ID}_${FAMILY_ID}/${PAR_2_ID}_${FAMILY_ID}/${PAR_2_ID}_${FAMILY_ID}-ready.bam
echo "...kid_bam = ${kid_bam}..."
echo "...par_1_bam = ${par_1_bam}..."
echo "...par_2_bam = ${par_2_bam}..."
# gather the variants in the DECIPHER file for which to generate bamouts
# chr is the second column - need to add the 'chr' prefix
# pos is the third column
# the first line is a header line, starting with 'Internal reference number or ID'
# file called: ${DEC_DIR}/<proband_id>_<fam_id>_DEC_FLT.csv
# and for each run GATK to generate the bamout files
# to be stored in ${BAMOUT_DIR}/${FAMILY_ID}
mkdir ${BAMOUT_DIR}/${FAMILY_ID}_${KID_ID}
var_file=${DEC_DIR}/${KID_ID}_${FAMILY_ID}_DEC_FLT.csv
echo "... reading ${var_file} to generate the bamouts..."
grep -v '^Internal' ${var_file} |
while IFS= read -r line
do
echo "$line"
IFS=, read -ra ary <<<"$line"
chr=${ary[1]}
pos=${ary[2]}
ref=${ary[4]}
alt=${ary[5]}
echo " --> chr = $chr, pos = $pos, ref = ${ref}, alt = ${alt}"
# generate the bamout file
echo "...doing the bamout"
echo " time ${GATK4} HaplotypeCaller --reference ${REFERENCE_GENOME} --input ${kid_bam} --input ${par_1_bam} --input ${par_2_bam} -L chr${chr}:${pos} --interval-padding 500"
echo " --active-probability-threshold 0.000 -ploidy 2"
echo " --output ${BAMOUT_DIR}/${FAMILY_ID}_${KID_ID}/${FAMILY_ID}_chr${chr}_${pos}.bamout.vcf -bamout ${BAMOUT_DIR}/${FAMILY_ID}_${KID_ID}/${FAMILY_ID}_chr${chr}_${pos}.bamout.bam"
time ${GATK4} HaplotypeCaller --reference ${REFERENCE_GENOME} --input ${kid_bam} --input ${par_1_bam} --input ${par_2_bam} -L chr${chr}:${pos} --interval-padding 500 \
--active-probability-threshold 0.000 -ploidy 2 \
--output ${BAMOUT_DIR}/${FAMILY_ID}_${KID_ID}/${FAMILY_ID}_chr${chr}_${pos}.bamout.vcf -bamout ${BAMOUT_DIR}/${FAMILY_ID}_${KID_ID}/${FAMILY_ID}_chr${chr}_${pos}.bamout.bam
done
#################################################################
# write the IGV batch file for this family based on the bamouts #
# to be stored as /scratch/u035/u035/shared/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${KID_ID}_${FAMILY_ID}.snapshot.txt #
#################################################################
snap_file=/home/u035/u035/shared/analysis/work/${PROJECT_ID}/DECIPHER/IGV/bamout_${KID_ID}_${FAMILY_ID}.snapshot.txt
# check if previous version exist, if so - delete it
if [ -f "${snap_file}" ]; then
echo "previous version of ${snap_file} exist --> deleted"
rm ${snap_file}
fi
# write the header for the IGV batch file
echo "new" >> ${snap_file}
echo "genome hg38" >> ${snap_file}
echo "snapshotDirectory \"/home/u035/u035/shared/analysis/work/${PROJECT_ID}/DECIPHER/IGV/${PLATE_ID}_${FAMILY_ID}_${KID_ID}\"" >> ${snap_file}
echo "" >> ${snap_file}
# now, go again over the variants in the DECIPHER file and generate one snapshot file for all the variants
var_file=${DEC_DIR}/${KID_ID}_${FAMILY_ID}_DEC_FLT.csv
echo "... reading ${var_file} to generate the IGV batch file using the bamouts..."
grep -v '^Internal' ${var_file} |
while IFS= read -r line
do
IFS=, read -ra ary <<<"$line"
chr=${ary[1]}
pos=${ary[2]}
ref=${ary[4]}
alt=${ary[5]}
left=$((${pos}-25))
right=$((${pos}+25))
echo "new" >> ${snap_file}
echo "load ${BAMOUT_DIR}/${FAMILY_ID}_${KID_ID}/${FAMILY_ID}_chr${chr}_${pos}.bamout.bam" >> ${snap_file}
echo "preference SAM.SHADE_BASE_QUALITY true" >> ${snap_file}
echo "goto chr${chr}:${left}-${right}" >> ${snap_file}
echo "group SAMPLE" >> ${snap_file}
echo "sort base" >> ${snap_file}
echo "squish" >> ${snap_file}
echo "snapshot bamout_${KID_ID}_${FAMILY_ID}_chr${chr}_${pos}_${ref}_${alt}.png" >> ${snap_file}
echo "" >> ${snap_file}
echo "" >> ${snap_file}
done
echo "Generating of the IGV batch files based on bamouts - done!"
echo "snap_file = ${snap_file}"
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "+++ Variant prioritization of trio ${FAMILY_ID} with ${KID_ID} completed +++"
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
done
echo ""
echo ""
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "+++ Analysing QUAD family ${FAMILY_ID} as two trios: DONE! +++"
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo ""
echo ""
#######################################################################################
#######################################################################################
### analyze only the two affected siblings and identify shared variants in them ###
#######################################################################################
#######################################################################################
echo ""
echo ""
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "+++ Analysing QUAD family ${FAMILY_ID} for shared variants in the two affected siblings +++"
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo ""
echo ""
##########################################################
# generate the affacted siblings PED file #
# named: ${BATCH_ID}_${PLATE_ID}_${FAMILY_ID}_shared.ped #
##########################################################
quad_ped_file=${BATCH_ID}_${PLATE_ID}_${FAMILY_ID}.ped
time ${PYTHON2} ${SCRIPTS_DIR}/generate_aff_sib_PED_from_quad.py ${PED_DIR} ${quad_ped_file} ${KID_1_ID} ${KID_2_ID}
##########################################################################
# generate the affected siblings VCF file #
# named: ${PLATE_ID}_${FAMILY_ID}_shared-gatk-haplotype-annotated.vcf.gz #
##########################################################################
quad_vcf_file=${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz
shared_vcf_file=${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared-gatk-haplotype-annotated.vcf.gz
# tabix index the quad file just in case
time ${TABIX} -p vcf ${quad_vcf_file}
# extract a VCF for these two kids
time java -Xmx24g -jar ${GATK3} -T SelectVariants \
-R ${REFERENCE_GENOME} \
-V ${quad_vcf_file} \
-sn ${KID_1_ID}_${FAMILY_ID} \
-sn ${KID_2_ID}_${FAMILY_ID} \
-jdk_deflater \
-jdk_inflater \
-o ${shared_vcf_file} \
-env
###############################################################################
### DNU and clean the the siblings VCF ###
### format: ${PLATE_ID}_${FAMILY_ID}_shared-gatk-haplotype-annotated.vcf.gz ###
###############################################################################
echo ""
echo ""
echo "Performing DNU and cleaning of the ${PLATE_ID}_${FAMILY_ID}_shared's VCF file..."
time ${VT} decompose -s ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared-gatk-haplotype-annotated.vcf.gz -o ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.decomp.vcf.gz
time ${VT} normalize ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.decomp.vcf.gz -r ${REFERENCE_GENOME} -o ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.norm.vcf.gz
time ${VT} uniq ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.norm.vcf.gz -o ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.DNU.vcf.gz
# remove sites with AC=0
time ${BCFTOOLS} view --min-ac=1 --no-update ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.DNU.vcf.gz > ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.AC0.vcf
# reset GT to no-call if num_ALT < num_ALT_THERSH or VAF < VAF_THRESH and GT != 0/0
# exlude variants from the blacklist (matching on chr,pos,ref,alt)
time ${PYTHON2} ${SCRIPTS_DIR}/filter_LQ_GT.py ${BLACKLIST} ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.AC0.vcf ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.clean.vcf
# bgzip and tabix it
time cat ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.clean.vcf | ${BGZIP} > ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.ready.vcf.gz
time ${TABIX} -p vcf ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.ready.vcf.gz
# delete intermediate files
rm ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared-gatk-haplotype-annotated.vcf.gz
rm ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.decomp.vcf.gz*
rm ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.norm.vcf.gz*
rm ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.DNU.vcf.gz*
rm ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.AC0.vcf
# to avoid bgzip pipe broken annoying, but not problematic message - skip the next step, the file will be used by G2P as IN_FILE and will be deleted last
# rm ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.clean.vcf
echo ""
echo ""
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo "DNU, AC=0, num_ALT & VAF & blacklist cleaning and of the ${PLATE_ID}_${FAMILY_ID}_shared's VCF file: done"
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo ""
echo ""
################################################################
### run G2P for the two affected siblings (DD genes) ###
### format: ${PLATE_ID}_${FAMILY_ID}_shared.clean.vcf ###
################################################################
echo "Performing G2P analysis (DD genes)for FAMILY_ID = ${PLATE_ID}_${FAMILY_ID}_shared..."
echo "Using ${TARGETS}"
IN_FILE=${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.clean.vcf
G2P_LOG_DIR=${G2P_DIR}/${PLATE_ID}_${FAMILY_ID}_shared_LOG_DIR
mkdir ${G2P_LOG_DIR}
TXT_OUT=${G2P_LOG_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.report.txt
HTML_OUT=${G2P_LOG_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.report.html
VCF_KEYS='gnomADe_r2.1.1_GRCh38|gnomADg_r3.1.1_GRCh38'
time ${VEP} \
-i ${IN_FILE} \
--output_file ${G2P_LOG_DIR}/${PLATE_ID}_${FAMILY_ID}_shared_inter_out.txt \
--force_overwrite \
--assembly GRCh38 \
--fasta ${REFERENCE_GENOME} \
--offline \
--merged \
--use_given_ref \
--cache --cache_version 100 \
--dir_cache /home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/vep \
--individual all \
--transcript_filter "gene_symbol in /home/u035/u035/shared/resources/G2P/genes_in_DDG2P.20210706.txt" \
--dir_plugins /home/u035/u035/shared/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
--plugin G2P,file='/home/u035/u035/shared/resources/G2P/DDG2P.20210706.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
echo ""
echo ""
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo "G2P analysis of FAMILY_ID = ${PLATE_ID}_${FAMILY_ID}_shared: done"
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo ""
########################################################
### run coverage for each proband (DD genes) ###
### already did it as part of the trio analysis ###
########################################################
###################################################################################
### for each proband generate the DECIPHER file ###
### ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.ready.vcf.gz - the sibling VCF ###
### ${TRANS_MAP} - the current transcript mapping file ###
###################################################################################
echo "Generating the DECIPHER file for all probands in ${FAMILY_ID} ..."
# first, split the family VCF to individual VCFs
# -c1: minimum allele count (INFO/AC) of sites to be printed
# split multi-allelic sites (by -m -any)
# left-alignment and normalization (by adding the -f)
file=${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.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
# create the names of the needed files
PED_FILE=${PED_DIR}/${BATCH_ID}_${PLATE_ID}_${FAMILY_ID}_shared.ped
IN_G2P_FILE=${G2P_DIR}/${PLATE_ID}_${FAMILY_ID}_shared_LOG_DIR/${PLATE_ID}_${FAMILY_ID}_shared.report.txt
FAM_IGV_DIR=${IGV_DIR}/${PLATE_ID}_${FAMILY_ID}_shared
FAM_BAM_DIR=${SOURCE_DIR}/${BATCH_NUM}_${VERSION_N}/families/????-??-??_${BATCH_NUM}_${VERSION_N}_${PLATE_ID}_${FAMILY_ID}
## call the python scrpit
time ${PYTHON2} ${SCRIPTS_DIR}/generate_DEC_IGV_aff_sib_scripts_from_quad.py \
${DECIPHER_ID} \
${TRANS_MAP} \
${PED_FILE} \
${IN_G2P_FILE} \
${FAM_IGV_DIR} \
${VCF_DIR} \
${PLATE_ID} \
${FAMILY_ID} \
${DEC_DIR} \
${FAM_BAM_DIR}
#############################################################################################################################
## using the DECIPHER bulk upload file v9 for each proband --> generate the DECIPHER bulk upload file v10 for each proband ##
#############################################################################################################################
# from the VCF, get all IDs (in the format probad_family_id), they are all affected probands (already checked at the start)
# INDI_ID is in format ${PROBAND_ID}_${FAMILY_ID}
file=${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.ready.vcf.gz
for INDI_ID in `${BCFTOOLS} query -l $file`; do
#################################
##### for each proband ####
#################################
echo "...Generating v10 Decipher bulk upload file for proband = ${INDI_ID} ...."
time ${PYTHON3} ${SCRIPTS_DIR}/convert_DEC_to_v10.py ${DEC_DIR} ${INDI_ID}_shared
done
echo ""
echo ""
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo "DECIPHER analysis of all probands in ${FAMILY_ID}: done"
echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
echo ""
echo ""
#rm ${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.clean.vcf
##############################################################################################
### for each of the affected probands ###
### for each variant in the DECIPHER upload file (only the shared variants) ###
### generate a IGV snapshot based on the realigned BAM used by GATK for calling variants ###
### first, generate BAMOUTs for each variant (to be stored in the BAMOUT folder) ###
### then, generate a batch script for IGV to produce the snapshots based on the BAMOUTs ###
##############################################################################################
echo ""
echo ""
echo "Generating the BAMOUT files for the ${FAMILY_ID} family ...."
# get the ids of the affected probands to generate the part of the command line which refers to the BAM files to by analysed
file=${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.ready.vcf.gz
# INDI_ID is in format ${PROBAND_ID}_${FAMILY_ID}
aff_pro_arr=()
for INDI_ID in `${BCFTOOLS} query -l $file`; do
aff_pro_arr+=(${INDI_ID})
done
echo " Found ${#aff_pro_arr[@]} affected probands in ${FAMILY_ID} for which BAMOUTs to be generated"
for key in "${!aff_pro_arr[@]}"; do
echo " ${aff_pro_arr[$key]}";
#~# INPUT_BAM_LINE=${INPUT_BAM_LINE}" --input ${SOURCE_DIR}/????-??-??_${VERSION_N}_${BATCH_ID}_${PLATE_ID}_${FAMILY_ID}/${aff_pro_arr[$key]}/${aff_pro_arr[$key]}-ready.bam"
INPUT_BAM_LINE=${INPUT_BAM_LINE}" --input ${SOURCE_DIR}/${BATCH_NUM}_${VERSION_N}/families/????-??-??_${BATCH_NUM}_${VERSION_N}_${PLATE_ID}_${FAMILY_ID}/${aff_pro_arr[$key]}/${aff_pro_arr[$key]}-ready.bam"
done
# now go over the shared G2P variants in the for which to generate bamouts
# the variants should be identical in the DECIPHER files for all affected individuals, pick the first individual
# chr is the second column - need to add the 'chr' prefix
# pos is the third column
# the first line is a header line, starting with 'Internal reference number or ID'
# file called: ${DEC_DIR}/<proband_id>_<fam_id>_shared_DEC_FLT.csv
# and for each run GATK to generate the bamout files
# to be stored in ${BAMOUT_DIR}/${FAMILY_ID}_shared
mkdir ${BAMOUT_DIR}/${FAMILY_ID}_shared
var_file=${DEC_DIR}/${aff_pro_arr[0]}_shared_DEC_FLT.csv
echo "... reading the shared variants in ${var_file} to generate the bamouts for each ..."
grep -v '^Internal' ${var_file} |
while IFS= read -r line
do
echo ""
echo ""
echo ""
echo "$line"
IFS=, read -ra ary <<<"$line"
chr=${ary[1]}
pos=${ary[2]}
ref=${ary[4]}
alt=${ary[5]}
echo " --> chr = $chr, pos = $pos, ref = ${ref}, alt = ${alt}"
# generate the bamout file
echo "...doing the bamout"
echo " time ${GATK4} HaplotypeCaller --reference ${REFERENCE_GENOME} ${INPUT_BAM_LINE}"
echo " -L chr${chr}:${pos} --interval-padding 500 --active-probability-threshold 0.000 -ploidy 2"
echo " --output ${BAMOUT_DIR}/${FAMILY_ID}_shared/${FAMILY_ID}_chr${chr}_${pos}.bamout.vcf -bamout ${BAMOUT_DIR}/${FAMILY_ID}_shared/${FAMILY_ID}_chr${chr}_${pos}.bamout.bam"
time ${GATK4} HaplotypeCaller --reference ${REFERENCE_GENOME} ${INPUT_BAM_LINE} -L chr${chr}:${pos} --interval-padding 500 \
--active-probability-threshold 0.000 -ploidy 2 \
--output ${BAMOUT_DIR}/${FAMILY_ID}_shared/${FAMILY_ID}_chr${chr}_${pos}.bamout.vcf -bamout ${BAMOUT_DIR}/${FAMILY_ID}_shared/${FAMILY_ID}_chr${chr}_${pos}.bamout.bam
done
##############################################################################################
## write the IGV batch file for each affected individual in this family based on the bamouts #
## to be stored as /home/u035/u035/shared/analysis/work/${PROJECT_ID}/DECIPHER/IGV/bamout_${PROBAND_ID}_${FAMILY_ID}.shared.snapshot.txt #
## ${PROBAND_ID}_${FAMILY_ID} == ${aff_pro_arr[$key] #
##################################################################
for key in "${!aff_pro_arr[@]}"; do
echo ""
echo ""
echo "Generating the IGV batch file for ${aff_pro_arr[$key]}";
#~# snap_file=/scratch/u035/u035/shared/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${aff_pro_arr[$key]}.shared.snapshot.txt
snap_file=/home/u035/u035/shared/analysis/work/${PROJECT_ID}/DECIPHER/IGV/bamout_${aff_pro_arr[$key]}.shared.snapshot.txt
# check if previous version exist, if so - delete it
if [ -f "${snap_file}" ]; then
echo "previous version of ${snap_file} exist --> deleted"
rm ${snap_file}
fi
# write the header for the IGV batch file
echo "new" >> ${snap_file}
echo "genome hg38" >> ${snap_file}
echo "snapshotDirectory \"/home/u035/u035/shared/analysis/work/${PROJECT_ID}/DECIPHER/IGV/${PLATE_ID}_${FAMILY_ID}_shared\"" >> ${snap_file}
echo "" >> ${snap_file}
# now, go again over the variants in this individual's DECIPHER file and generate one snapshot file for all the variants
var_file=${DEC_DIR}/${aff_pro_arr[$key]}_shared_DEC_FLT.csv
echo "... reading ${var_file} to generate the IGV batch file using the bamouts..."
grep -v '^Internal' ${var_file} |
while IFS= read -r line
do
IFS=, read -ra ary <<<"$line"
chr=${ary[1]}
pos=${ary[2]}
ref=${ary[4]}
alt=${ary[5]}
left=$((${pos}-25))
right=$((${pos}+25))
echo "new" >> ${snap_file}
echo "load ${BAMOUT_DIR}/${FAMILY_ID}_shared/${FAMILY_ID}_chr${chr}_${pos}.bamout.bam" >> ${snap_file}
echo "preference SAM.SHADE_BASE_QUALITY true" >> ${snap_file}
echo "goto chr${chr}:${left}-${right}" >> ${snap_file}
echo "group SAMPLE" >> ${snap_file}
echo "sort base" >> ${snap_file}
echo "squish" >> ${snap_file}
echo "snapshot bamout_${aff_pro_arr[$key]}_shared_chr${chr}_${pos}_${ref}_${alt}.png" >> ${snap_file}
echo "" >> ${snap_file}
echo "" >> ${snap_file}
done
echo "Generating of the IGV batch file based on bamouts for ${aff_pro_arr[$key]}- done!"
echo "snap_file = ${snap_file}"
done
echo ""
echo ""
echo ""
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "+++ Variant prioritization of family ${FAMILY_ID} as affected sib-pair completed +++"
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo ""
echo ""
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "+++ Analysing QUAD family ${FAMILY_ID} for shared variants in the two affected siblings: DONE! +++"
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo ""
echo ""