mavis

MAVIS workflow, annotation of structural variants. An application framework for the rapid generation of structural variant consensus, able to visualize the genetic impact and context as well as process both genome and transcriptome data.

Overview

Dependencies

Usage

Cromwell

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

Inputs

Required workflow parameters:

Parameter	Value	Description
`sampleId`	String	sample identifier, which will be used for final naming of output files
`inputBAMs`	Array[BamData]	Collection of alignment files with indexes and metadata
`svData`	Array[SvData]	Collection of SV calls with metadata
`reference`	String	The genome reference build. for example: hg19, hg38

Optional workflow parameters:

Parameter	Value	Default	Description

Optional task parameters:

Parameter	Value	Default	Description
`filterDellyInput.jobMemory`	Int	12	Memory allocated for this job
`filterDellyInput.timeout`	Int	5	Timeout in hours, needed to override imposed limits
`filterDellyInput.svFileBase`	String	basename(svFile,".vcf.gz")	the basename of the file, needed to form the output file name
`runMavis.outputCONFIG`	String	"mavis_config.cfg"	name of config file for MAVIS
`runMavis.scriptName`	String	"mavis_config.sh"	name for bash script to run mavis configuration, default mavis_config.sh
`runMavis.mavisAligner`	String	"blat"	blat by default, may be customized
`runMavis.mavisScheduler`	String	"SGE"	Our cluster environment, sge, SLURM etc.
`runMavis.mavisDrawFusionOnly`	String	"False"	flag for MAVIS visualization control
`runMavis.mavisAnnotationMemory`	Int	32000	Memory allocated for annotation step
`runMavis.mavisValidationMemory`	Int	32000	Memory allocated for validation step
`runMavis.mavisTransValidationMemory`	Int	32000	Memory allocated for transvalidation step
`runMavis.mavisMemoryLimit`	Int	32000	Max Memory allocated for MAVIS
`runMavis.mavisQueue`	String	"u20.q"	the mavis job queue
`runMavis.minClusterPerFile`	Int	10	Determines the way parallel calculations are organized
`runMavis.drawNonSynonymousCdnaOnly`	String	"False"	flag for MAVIS visualization control
`runMavis.mavisUninformativeFilter`	String	"True"	Should be enabled if used is only interested in events inside genes, speeds up calculations
`runMavis.jobMemory`	Int	12	Memory allocated for this job
`runMavis.sleepInterval`	Int	20	A pause after scheduling step, in seconds
`runMavis.timeout`	Int	24	Timeout in hours, needed to override imposed limits
`runMavis.maxBins`	Int	100000	Maximum value for transcriptome_bins and genome_bins parameters, Default is 100000
`runMavis.mavisMaxTime`	Int	timeout * 1800	Timeout for MAVIS tasks, in seconds. 1/2 of the timeout

Outputs

Output	Type	Description
`summary`	File	File with copy number variants, native varscan format
`drawings`	File	Plots generated with MAVIS, collected into a single tar.gz archive
`nscvWT`	File?	Whole transcriptome non-synonymous coding variants. The output file is only generated if variants are found
`nscvWG`	File?	Whole genome non-synonymous coding variants. The output file is only generated if variants are found

Commands

This section lists command(s) run by WORKFLOW workflow

Running mavis

MAVIS annotates structural variants for WG and WT experiments

OPTIONAL : Filter Delly files to keep ONLY the PASS calls

    bcftools view -i "%FILTER='PASS'" ~{svFile} -Oz -o ~{svFileBase}.pass.vcf.gz

Setup Mavis : Inline python code

    unset LD_LIBRARY_PATH
    unset LD_LIBRARY_PATH_modshare
    export MAVIS_REFERENCE_GENOME=~{referenceGenome}
    export MAVIS_ANNOTATIONS=~{annotations}
    export MAVIS_MASKING=~{masking}
    export MAVIS_DGV_ANNOTATION=~{dvgAnnotations}
    export MAVIS_ALIGNER_REFERENCE=~{alignerReference}
    export MAVIS_TEMPLATE_METADATA=~{templateMetadata}
    export MAVIS_TIME_LIMIT=~{mavisMaxTime}
    python <<CODE

    libtypes = {'WT': "transcriptome", 'MR': "transcriptome", 'WG': "genome"}
    wfMappings = {'StructuralVariation': 'delly', 'delly': 'delly', 'arriba' : 'arriba', 'StarFusion': 'starfusion', 'manta': 'manta'}

    b = "~{sep=' ' inputBAMs}"
    bams = b.split()
    l = "~{sep=' ' libTypes}"
    libs = l.split()
    s = "~{sep=' ' svData}"
    svdata = s.split()
    w = "~{sep=' ' svWorkflows}"
    wfs = w.split()
    sl = "~{sep=' ' svLibDesigns}"
    svlibs = sl.split()

    library_lines = []
    convert_lines = []
    assign_lines = []
    assign_arrays = {}
    for lt in libtypes.keys():
     assign_arrays[lt] = []

    for b in range(len(bams)):
     flag = ('False' if libs[b] == 'WG' else 'True')
     library_lines.append( "--library " + libs[b] + ".~{sid} " + libtypes[libs[b]] + " diseased " + flag + " " + bams[b] + " \\\\" )


    for s in range(len(svdata)):
     for w in wfMappings.keys():
         if w in wfs[s]:
             if w == 'arriba':
                 convert_lines.append( "--external_conversion arriba \"~{arribaConverter}  " + svdata[s] + "\"" + " \\\\" )
             else:
                 convert_lines.append( "--convert " + wfMappings[w] + " " + svdata[s] + " " + wfMappings[w] + " \\\\" )
             assign_arrays[svlibs[s]].append(wfMappings[w])

    for b in range(len(bams)):
       if len(assign_arrays[libs[b]]) > 0:
           separator = " "
           tools = separator.join(assign_arrays[libs[b]])
           assign_lines.append( "--assign " + libs[b] + ".~{sid} " + tools + " \\\\" )

    f = open("~{scriptName}","w+")
    f.write("#!/bin/bash" + "\n\n")
    f.write('mavis config \\\\\n')
    f.write('\n'.join(library_lines) + '\n')
    f.write('\n'.join(convert_lines) + '\n')
    f.write('\n'.join(assign_lines) + '\n')
    f.write("--write ~{outputCONFIG}\n")
    f.close()
    CODE

Run Mavis

    chmod +x ~{scriptName}
    ./~{scriptName}
    export MAVIS_ALIGNER='~{mavisAligner}'
    export MAVIS_SCHEDULER=~{mavisScheduler}
    export MAVIS_DRAW_FUSIONS_ONLY=~{mavisDrawFusionOnly}
    export MAVIS_ANNOTATION_MEMORY=~{mavisAnnotationMemory}
    export MAVIS_VALIDATION_MEMORY=~{mavisValidationMemory}
    export MAVIS_TRANS_VALIDATION_MEMORY=~{mavisTransValidationMemory}
    export MAVIS_MEMORY_LIMIT=~{mavisMemoryLimit}
    export DRAW_NON_SYNONYMOUS_CDNA_ONLY=~{drawNonSynonymousCdnaOnly}
    export min_clusters_per_file=~{minClusterPerFile}
    export MAVIS_UNINFORMATIVE_FILTER=~{mavisUninformativeFilter}
    mavis setup ~{outputCONFIG} -o .
    BATCHID=$(grep MS_batch build.cfg | grep -v \] | sed s/.*-// | tail -n 1)
    mavis schedule -o . --submit 2> >(tee launch_stderr.log)

Compile results. Drawings and Legends are collected into a single zip archive.

Support

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

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oicr-gsi/mavis