# load all the softwares
module load IN-BIOS5000/HT-2022
module load R/4.1.2-foss-2021b

# create folder structure
mkdir -p results/00_fastq
mkdir -p results/01_alignment
mkdir -p results/02_refineAlignment
mkdir -p results/03_variantcalling
mkdir -p results/04_variantfiltration
cp -r /projects/ec34/in-biosx000/human_vc/scripts .

# copy the fastq files to local 00_fastq folder
cp /projects/ec34/in-biosx000/human_vc/results/00_fastq/* results/00_fastq

# running alignment under the local 01_alignment folder
cd results/01_alignment
bash ../../scripts/01_bwa.bash \
../00_fastq/NA12878N47F_S47_R1_001.fastq.gz \
../00_fastq/NA12878N47F_S47_R2_001.fastq.gz \
NA12878F \
2>bwa.log

# running mark duplicates under the local 02_refineAlignment folder
cd ../02_refineAlignment
bash ../../scripts/02_markdup.bash \
../01_alignment/sorted.bam \
NA12878F.bam \
2>markdup.log

# running quality control on the bam file under the local 02_refineAlignment
bash ../../scripts/03_bam_qc.bash \
NA12878F.bam \
NA12878F \
/projects/ec34/in-biosx000/human_vc/metadata/regions/target.interval_list \
/projects/ec34/in-biosx000/human_vc/metadata/regions/probe.interval_list \
2>bam_qc.log


# running variant calling on the bam file under the local 03_variantcalling
cd ../03_variantcalling
bash ../../scripts/04_variantCalling.bash \
../02_refineAlignment/NA12878F.bam \
NA12878F \
/projects/ec34/in-biosx000/human_vc/metadata/regions/NexteraRapidCapture-181702-probeTarget.merged.sort.interval_list \
2>variantcalling.log

# running variant filtration on the raw vcf file under the local 04_variantfiltration
cd ../04_variantfiltration
bash ../../scripts/05_variantfiltration.bash \
../03_variantCalling/NA12878F.raw.vcf.gz \
NA12878F \
2>variantfiltration.log

# predict de novo variants from trio data
module load BCFtools/1.10.2-GCC-8.3.0
export BCFTOOLS_PLUGINS=/projects/ec34/in-biosx000/human_vc/tools/bcftools/plugins/
bcftools +trio-dnm2 -P HG002.ped --with-pPL HG002.filter.vcf > HG002.filter.denovo.vcf