VCFscripts.txt

Trimmomatic
$For sp in {1..100}; do
> java -jar trimmomatic-0.39.jar PE -threads 8 -phred33 -trimlog log.txt  /home/thanh/Desktop/gatk/work/sample/100KHV/VT${sp}_R1.fastq.gz /home/thanh/Desktop/gatk/work/sample/100KHV/VT${sp}_R2.fastq.gz /home/thanh/Desktop/gatk/work/QC/VT${sp}_QC_paired_1.fastq.gz /home/thanh/Desktop/gatk/work/QC/VT${sp}_QC_unpaired_1.fastq.gz /home/thanh/Desktop/gatk/work/QC/VT${sp}_QC_paired_2.fastq.gz  /home/thanh/Desktop/gatk/work/QC/VT${sp}_QC_unpaired_2.fastq.gz ILLUMINACLIP:adapters/TruSeq3-PE-2.fa:2:30:3:1:true LEADING:20 TRAILING:20 SLIDINGWINDOW:3:15 AVGQUAL:20 MINLEN:100;
> Done
Mapping
$for sp in {1..100}; do
> bwa mem -t 4 -M -R "@RG\tID:100PGx\tSM:VT${sp}\tPL:illumina\tLB:lib1\tPU:unit1" /home/thanh/Desktop/gatk/work/refgen/resources-broad-hg38-v0-Homo_sapiens_assembly38.fasta /home/thanh/Desktop/gatk/work/QC/VT${sp}_QC_paired_1.fastq.gz /home/thanh/Desktop/gatk/work/QC/VT${sp}_QC_paired_2.fastq.gz |samtools view -bS -o /home/thanh/Desktop/gatk/work/map38/VT${sp}_map.bam;
> done
MarkDuplicates (picard)
$java -jar picard.jar MarkDuplicates I=/home/thanh/Desktop/gatk/work/map38/VT${sp}_map.bam O=/home/thanh/Desktop/gatk/work/dup38/VT${sp}_marked.bam M=/home/thanh/Desktop/gatk/work/dup38/Dup${sp}.txt ASO=queryname
$java -jar picard.jar SortSam I=/home/thanh/Desktop/gatk/work/dup38/VT${sp}_marked.bam O=/home/thanh/Desktop/gatk/work/dup38/VT${sp}_sorted.bam SORT_ORDER=coordinate
Base Recalibration (gatk4)
$gatk BaseRecalibrator -I /home/thanh/Desktop/gatk/work/dup38/VT${sp}_sorted.bam -R /home/thanh/Desktop/gatk/work/refgen/resources-broad-hg38-v0-Homo_sapiens_assembly38.fasta --known-sites /home/thanh/Desktop/gatk/work/refgen/resources-broad-hg38-v0-Homo_sapiens_assembly38.dbsnp138.vcf -O /home/thanh/Desktop/gatk/work/nm.recal38/VT${sp}_data.table
$gatk ApplyBQSR -R /home/thanh/Desktop/gatk/work/refgen/resources-broad-hg38-v0-Homo_sapiens_assembly38.fasta -I /home/thanh/Desktop/gatk/work/dup38/VT${sp}_sorted.bam --bqsr-recal-file /home/thanh/Desktop/gatk/work/s.recal38/VT${sp}_data.table -O /home/thanh/Desktop/gatk/work/s.recal38/reVT${sp}.bam
Variants calling (Haplotypecaller)
#gVCF
$java -jar -Xmx2g /home/thanh/Desktop/gatk/work/gatk/gatk-package-4.1.4.1-local.jar HaplotypeCaller -R /home/thanh/Desktop/gatk/work/refgen/resources-broad-hg38-v0-Homo_sapiens_assembly38.fasta -I /home/thanh/Desktop/gatk/work/s.recal38/rdVT${sp}.bam -L /home/thanh/Desktop/gatk/work/CDS100genes.list.bed -O /home/thanh/Desktop/gatk/work/vcf38/VT${sp}.g.vcf.gz -ERC GVCF
SNPs
$java -jar -Xmx2g /home/thanh/Desktop/gatk/work/gatk/gatk-package-4.1.4.1-local.jar HaplotypeCaller -R /home/thanh/Desktop/gatk/work/refgen/resources-broad-hg38-v0-Homo_sapiens_assembly38.fasta -I /home/thanh/Desktop/gatk/work/s.recal38/rdVT${sp}.bam -L /home/thanh/Desktop/gatk/work/CDS100genes.list.bed -O /home/thanh/Desktop/gatk/work/vcf38/VT${sp}.vcf.gz

$java -jar -Xmx2g /home/thanh/Desktop/gatk/work/gatk/gatk-package-4.1.4.1-local.jar HaplotypeCaller -R /home/thanh/Desktop/gatk/work/refgen/resources-broad-hg38-v0-Homo_sapiens_assembly38.fasta -I /home/thanh/Desktop/gatk/work/s.recal38/rdVT1.bam -L /home/thanh/Desktop/gatk/work/pgx.interval.file.list -O /home/thanh/Desktop/gatk/work/vcf38/testpc.VT1.vcf.gz --output-mode EMIT_ALL_ACTIVE_SITES

Joint Cohort
#consolidate gVCF
$java -jar -Xmx2g /home/thanh/Desktop/gatk/work/gatk/gatk-package-4.1.4.1-local.jar GenomicsDBImport -V vcf38/VT1.vcf.gz  -V vcf38/VT2.g.vcf.gz -V vcf38/VT3.g.vcf.gz -V vcf38/VT4.g.vcf.gz -V vcf38/VT5.g.vcf.gz -V vcf38/VT6.g.vcf.gz -V vcf38/VT7.g.vcf.gz -V vcf38/VT8.g.vcf.gz -V vcf38/VT9.g.vcf.gz -V vcf38/VT10.g.vcf.gz -V vcf38/VT11.g.vcf.gz  -V vcf38/VT12.g.vcf.gz -V vcf38/VT13.g.vcf.gz -V vcf38/VT14.g.vcf.gz -V vcf38/VT15.g.vcf.gz -V vcf38/VT16.g.vcf.gz -V vcf38/VT17.g.vcf.gz -V vcf38/VT18.g.vcf.gz -V vcf38/VT19.g.vcf.gz -V vcf38/VT20.g.vcf.gz -V vcf38/VT21.g.vcf.gz  -V vcf38/VT22.g.vcf.gz -V vcf38/VT23.g.vcf.gz -V vcf38/VT24.g.vcf.gz -V vcf38/VT25.g.vcf.gz -V vcf38/VT26.g.vcf.gz -V vcf38/VT27.g.vcf.gz -V vcf38/VT28.g.vcf.gz -V vcf38/VT29.g.vcf.gz -V vcf38/VT30.g.vcf.gz -V vcf38/VT31.g.vcf.gz  -V vcf38/VT32.g.vcf.gz -V vcf38/VT33.vcf.gz -V vcf38/VT34.vcf.gz -V vcf38/VT35.g.vcf.gz -V vcf38/VT36.g.vcf.gz -V vcf38/VT37.g.vcf.gz -V vcf38/VT38.g.vcf.gz -V vcf38/VT39.g.vcf.gz -V vcf38/VT40.g.vcf.gz -V vcf38/VT41.g.vcf.gz  -V vcf38/VT42.g.vcf.gz -V vcf38/VT43.g.vcf.gz -V vcf38/VT44.g.vcf.gz -V vcf38/VT45.g.vcf.gz -V vcf38/VT46.g.vcf.gz -V vcf38/VT47.g.vcf.gz -V vcf38/VT48.g.vcf.gz -V vcf38/VT49.g.vcf.gz -V vcf38/VT50.g.vcf.gz -V vcf38/VT51.g.vcf.gz  -V vcf38/VT52.g.vcf.gz -V vcf38/VT53.g.vcf.gz -V vcf38/VT55.g.vcf.gz -V vcf38/VT56.g.vcf.gz -V vcf38/VT57.g.vcf.gz -V vcf38/VT58.g.vcf.gz -V vcf38/VT59.g.vcf.gz -V vcf38/VT60.g.vcf.gz -V vcf38/VT61.vcf.gz  -V vcf38/VT62.g.vcf.gz -V vcf38/VT63.g.vcf.gz -V vcf38/VT64.g.vcf.gz -V vcf38/VT65.g.vcf.gz -V vcf38/VT66.g.vcf.gz -V vcf38/VT67.g.vcf.gz -V vcf38/VT68.g.vcf.gz -V vcf38/VT69.g.vcf.gz -V vcf38/VT70.g.vcf.gz -V vcf38/VT71.g.vcf.gz  -V vcf38/VT72.g.vcf.gz -V vcf38/VT73.g.vcf.gz -V vcf38/VT74.g.vcf.gz -V vcf38/VT75.g.vcf.gz -V vcf38/VT76.g.vcf.gz -V vcf38/VT77.g.vcf.gz -V vcf38/VT78.g.vcf.gz -V vcf38/VT79.g.vcf.gz -V vcf38/VT80.g.vcf.gz -V vcf38/VT81.g.vcf.gz -V vcf38/VT82.g.vcf.gz -V vcf38/VT83.g.vcf.gz -V vcf38/VT84.g.vcf.gz -V vcf38/VT85.g.vcf.gz -V vcf38/VT86.g.vcf.gz -V vcf38/VT87.g.vcf.gz -V vcf38/VT88.g.vcf.gz -V vcf38/VT89.g.vcf.gz -V vcf38/VT90.g.vcf.gz -V vcf38/VT91.g.vcf.gz  -V vcf38/VT92.g.vcf.gz -V vcf38/VT93.g.vcf.gz -V vcf38/VT94.g.vcf.gz -V vcf38/VT95.g.vcf.gz -V vcf38/VT96.g.vcf.gz -V vcf38/VT97.g.vcf.gz -V vcf38/VT98.g.vcf.gz -V vcf38/VT99.g.vcf.gz -V vcf38/VT100.g.vcf.gz -V vcf38/VT54.g.vcf.gz --genomicsdb-workspace-path consolidate38 -L CDS100genes.list.bed
$java -jar gatk/gatk-package-4.1.4.1-local.jar GenotypeGVCFs -R refgen/resources-broad-hg38-v0-Homo_sapiens_assembly38.fasta -V gendb://consolidate38 -O 100KHV.vcf