sage

SAGE somatic variant calling workflow with Redux UMI processing and per-chromosome parallelization

Overview

Dependencies

• SAGE
• Redux
• GATK
• bcftools
• Samtools

Usage

Cromwell

java -jar cromwell.jar run sage.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter	Value	Description
tumour_bam	File	Input tumor BAM file
tumour_bai	File	Input tumor BAI index
normal_bam	File	Input normal BAM file
normal_bai	File	Input normal BAI index
donor	String	Patient/donor identifier

Optional workflow parameters:

Parameter	Value	Default	Description
genomeVersion	String	"38"	Genome version (only 38 supported)
use_redux	Boolean	false	Run Redux to generate UMI jitter files
chromosomes	Array[String]	["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"]	List of chromosomes to process in parallel
min_map_quality	Int	10	Minimum map quality
hard_min_tumor_qual	Int	50	Minimum hard threshold for tumor base quality
hard_min_tumor_raw_alt_support	Int	2	Minimum raw alternate allele support in tumor
hard_min_tumor_vaf	Float	0.002	Minimum tumor variant allele frequency

Optional task parameters:

Parameter	Value	Default	Description
extractTumorName.memory	Int	4	Memory in GB
extractTumorName.timeout	Int	4	Timeout in hours
extractNormalName.memory	Int	4	Memory in GB
extractNormalName.timeout	Int	4	Timeout in hours
reduxTumor.threads	Int	8	Number of threads
reduxTumor.memory	Int	16	Memory in GB
reduxTumor.timeout	Int	24	Timeout in hours
reduxNormal.threads	Int	8	Number of threads
reduxNormal.memory	Int	16	Memory in GB
reduxNormal.timeout	Int	24	Timeout in hours
sagePerChromosome.threads	Int	8	Number of threads
sagePerChromosome.memory	Int	40	Memory in GB
sagePerChromosome.timeout	Int	24	Timeout in hours
mergeVcfs.memory	Int	8	Memory in GB
mergeVcfs.timeout	Int	4	Timeout in hours
mergeBqrDirs.memory	Int	4	Memory in GB
mergeBqrDirs.timeout	Int	2	Timeout in hours

Outputs

Output	Type	Description	Labels
sage_vcf	File	Merged VCF file containing somatic variants from all chromosomes
sage_vcf_index	File	Index file for the merged VCF
sage_bqr_directory	File	Merged base quality recalibration directory
tumor_jitter	File?	Optional Redux jitter file for tumor sample
normal_jitter	File?	Optional Redux jitter file for normal sample

Commands

This section lists command(s) run by SAGE workflow

• Running SAGE

    set -euo pipefail
    gatk --java-options "-Xmx1g" GetSampleName \
      -R ~{refFasta} \
      -I ~{inputBam} \
      -O sample_name.txt \
      -encode

    set -euo pipefail
    
    # Run Redux to generate jitter file
    java -Xmx~{memory}G -jar /.mounts/labs/gsiprojects/gsi/gsiusers/gpeng/workflow/sage/test/redux_v1.2.2.jar \
    -sample ~{sample_name} \
    -input_bam ~{input_bam} \
    -ref_genome ~{refFasta} \
    -ref_genome_version 38 \
    -bamtool $SAMTOOLS_ROOT/bin/samtools \
    -threads ~{threads} \
    -log_level DEBUG \
    -output_dir ./
        
    java -jar redux.jar 
    -sample SAMPLE_ID 
    -input_bam SAMPLE_ID.lane_01.bam,SAMPLE_ID.lane_02.bam,SAMPLE_ID.lane_03.bam  
    -ref_genome /path_to_fasta_files/
    -ref_genome_version V37
    -unmap_regions /ref_data/unmap_regions.37.tsv
    -ref_genome_msi_file /ref_data/msi_jitter_sites.37.tsv.gz 
    -write_stats 
    -bamtool /path_to_samtools/ 
    -output_dir /path_to_output/
    -log_level DEBUG 
    -threads 24
    # Redux outputs: sample.redux.jitter.tsv

    set -euo pipefail
    
    mkdir -p ~{tumour_name}.sage.bqr
    
    java -Xmx32G -cp $SAGE_ROOT/sage.jar com.hartwig.hmftools.sage.SageApplication \
      -tumor ~{tumour_name} \
      -tumor_bam ~{tumour_bam} \
      -reference ~{reference_name} \
      -reference_bam ~{reference_bam} \
      -ref_genome_version 38 \
      -ref_genome ~{refFasta} \
      -ensembl_data_dir ~{ensemblDir} \
      -high_confidence_bed ~{highConfBed} \
      ~{if defined(tumor_jitter) then "-tumor_jitter " + tumor_jitter else ""} \
      ~{if defined(normal_jitter) then "-reference_jitter " + normal_jitter else ""} \
      -specific_chr ~{chromosome} \
      -output_vcf ~{tumour_name}.~{chromosome}.sage.vcf.gz \
      -threads ~{threads} \
      -min_map_quality ~{min_map_quality} \
      -hard_min_tumor_qual ~{hard_min_tumor_qual} \
      -hard_min_tumor_raw_alt_support ~{hard_min_tumor_raw_alt_support} \
      -hard_min_tumor_vaf ~{hard_min_tumor_vaf}

    # Move BQR files
    mv *.sage.bqr.tsv ~{tumour_name}.sage.bqr/ 2>/dev/null || true
    zip -r ~{tumour_name}.~{chromosome}.sage.bqr.zip ~{tumour_name}.sage.bqr/

    set -euo pipefail
    
    # Create file list for bcftools concat
    for vcf in ~{sep=' ' vcfs}; do
      echo "$vcf" >> vcf_list.txt
    done
    
    # Sort by chromosome order
    sort -V vcf_list.txt > vcf_list_sorted.txt
    
    # Concatenate VCFs in order
    bcftools concat \
      --file-list vcf_list_sorted.txt \
      --output-type z \
      --output ~{sample_name}.sage.vcf.gz
    
    # Index the merged VCF
    tabix -p vcf ~{sample_name}.sage.vcf.gz

    set -euo pipefail
    
    mkdir -p ~{sample_name}.sage.bqr
    
    # Unzip all BQR files into the same directory
    for bqr_zip in ~{sep=' ' bqr_zips}; do
      unzip -o "$bqr_zip" -d temp_bqr/
    done
    
    # Move all .tsv files to final directory
    find temp_bqr -name "*.sage.bqr.tsv" -exec mv {} ~{sample_name}.sage.bqr/ \;
    
    # Zip the merged directory
    zip -r ~{sample_name}.sage.bqr.zip ~{sample_name}.sage.bqr/

Support

For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .

Generated with generate-markdown-readme (https://github.com/oicr-gsi/gsi-wdl-tools/)