Documentation of pipeline for processing paired end reads of lpWGS data.
fastqc https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
picard https://github.com/broadinstitute/picard
bwa http://bio-bwa.sourceforge.net/bwa.shtml
trimmomatic http://www.usadellab.org/cms/?page=trimmomatic
samtools http://samtools.sourceforge.net/
GATK3: https://gatk.broadinstitute.org/hc/en-us
copywriteR: https://github.com/PeeperLab/CopywriteR
ichorCNA: https://github.com/broadinstitute/ichorCNA
CNApp: https://github.com/elifesciences-publications/CNApp
Requirements and Required Format:
Sample_ID
${Sample_ID}_R1.fastq.gz saved under "data/FASTQ"
${Sample_ID}_R2.fastq.gz saved under "data/FASTQ"
ucsc.hg_19.fastasaved under "data/hg19"
genome.fa bwa index reference genome saved under "data/hg19"
1000G_phase1.indels.hg19.sites.vcf hg19 known sites saved under "data/hg19"
dbsnp_138.hg19.vcf saved under hg19 known sites "data/hg19"
Mills_and_1000G_gold_standard.indels.hg19.sites.vcf hg19 known sites saved under "data/hg19"
hg19_100kb_chr CopywriteR Mapping Folder (provided)
Run lPWGS_pipeline.sh after specifying Sample_ID, adding ${Sample_ID}_R1.fastq.gz and ${Sample_ID}_R2.fastq.gz to data folder, adding the bwa index output of genome.fa, ucsc.hg_19.fasta, and hg19 known-sites to the hg19 folder in the hg19 resource bundle from GATK gs://gatk-legacy-bundles
FASTQC generated from FASTQ files for paired-end reads (R1 & R2) using fastqc for <Sample_ID>
fastqc /path/to/<Sample_ID_R1>.fastq.gz
fastqc /path/to/<Sample_ID_R2>.fastq.gz
Quality trimming and adapter clipping using Trimmomatic for FASTQ files <Sample_ID_R1> & <Sample_ID_R2>
java -jar /path/to/trimmomatic-0.39.jar PE -phred33 /path/to/<Sample_ID_R1>.fastq.gz /path/to/<Sample_ID_R2>.fastq.gz
/path/to/<Sample_ID_R1_P>.fastq.gz /path/to/<Sample_ID_R1_S>.fastq.gz /path/to/<Sample_ID_R2_P>.fastq.gz /path/to/<Sample_ID_R2_S>.fastq.gz
ILLUMINACLIP:/path/to/adapters/TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Align paired reads to hg19 genome and convert .FASTQ to .BAM using bwa mem and samtools view
bwa mem -t 4 hg19.fasta /path/to/<Sample_ID_R1_P>.fastq.gz /path/to/<Sample_ID_R2_P>.fastq.gz | samtools view -S -b - > /path/to/<Sample_ID>.bam
Coordinate sort .BAM file using samtools sort
samtools sort -O bam -@ 10 -o /path/to/<Sample_ID>.sorted.bam /path/to/<Sample_ID>.bam
Deduplicate sorted bam file (sorted.bam) using picard MarkDuplicates
java -jar /path/to/picard.jar MarkDuplicates REMOVE_DUPLICATES=true I=/path/to/<Sample_ID>.sorted.bam O=/path/to/<Sample_ID>.sorted_dedup.bam M=/path/to/<Sample_ID>.sorted_markdup_metrics.txt
Create index of deduplicated and sorted bam file (sorted_dedup.bam) using samtools index
samtools index /path/to/data/${Sample_ID}/$Sample_ID.sorted_dedup.bam
Perform indel realignment using GATK3 GenomeAnalysisTK RealignerTargetCreator and IndelRealigner
java -jar /path/to/GenomeAnalysisTK.jar -T RealignerTargetCreator -R /path/to/hg19.fasta -I /path/to/<Sample_ID>.sorted_dedup.bam -known /path/to/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz -known /path/to/1000G_phase1.indels.hg19.sites.vcf.gz -o /path/to/DG_517.sorted_dedup.IndelRealigner.intervals
java -jar /path/to/GenomeAnalysisTK.jar -T IndelRealigner -R /path/to/hg19.fasta -I /path/to/<Sample_ID>.sorted_dedup.bam -known /path/to/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz -known /path/to/1000G_phase1.indels.hg19.sites.vcf.gz --targetIntervals /path/to/DG_517.sorted_dedup.IndelRealigner.intervals -o /path/to/<Sample_ID>.sorted_dedup_realign.bam
Run base quality score recalibration using GATK3 BaseRecalibrator:
java -jar /path/to/GenomeAnalysisTK.jar -T BaseRecalibrator -R /path/to/ucsc.hg19.fasta -I /path/to/<Sample_ID>.sorted_dedup_realign.bam --knownSites /path/to/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz --knownSites /path/to/1000G_phase1.indels.hg19.sites.vcf.gz --knownSites /path/to/dbsnp_138.hg19.vcf.gz -o /path/to/<Sample_ID>.sorted_dedup_realign.recal_data.table
java -jar /path/to/GenomeAnalysisTK.jar -T PrintReads -R /path/to/hg19.fasta -I /path/to/<Sample_ID>.sorted_dedup_realign.bam --BQSR /path/to/Test_Pipeline/<Sample_ID>.sorted_dedup_realign.recal_data.table -o /path/to/<Sample_ID>.sorted_dedup_realign_BQSR.bam
Run CopywriteR
R -e "library(<Sample_ID>)" -e "Sample_ID <- '<Sample_ID>'" -e "bam_location <- file.path(getwd(),'data',Sample_ID, paste(Sample_ID,'sorted_dedup_realign_BQSR.bam',sep='.'))" -e "sample.control <- data.frame(bam_location, bam_location)" -e "bp.param <- SnowParam(workers = 12, type = 'SOCK')" -e "CopywriteR(sample.control = sample.control, destination.folder=file.path(getwd(),'data',Sample_ID), reference.folder= file.path(getwd(),'data','hg19','hg19_100kb_chr'), bp.param)" -e "plotCNA(destination.folder = file.path(getwd(),'data',Sample_ID))"
Run IchorCNA
script path/to/ichorCNA/scripts/runIchorCNA.R --id <Sample_ID> --WIG path/to/data/<Sample_ID>/<Sample_ID>.wig --outDir path/to/data/<Sample_ID> --gcWig path/to/programs/ichorCNA/inst/extdata/gc_hg19_1000kb.wig --normal 'c(0.5, 0.85, 0.995, 0.999)' --libdir /path/to/programs/ichorCNA
Run CNApp in browser with <Sample_ID>.CNApp__input.txt as input
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