GenomeSTRiP 2.0 don't have anything result about CNVDiscoveryPipeline.

Question

[sunhye0829]

Hi,

I have human whole genome sequencing data and I want to analyze copy-number variations.

So, I made subset which consists of chromosome20 ,and tested to call copy-number variation using CNVDiscoveryPipeline module in GenomeSTRiP2.0.

The CNVDiscoveryPipeline run was done successfully without error, but the results didn't exist anywhere.

My script is,

classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"

java -cp ${classpath} ${mx} \
    org.broadinstitute.gatk.queue.QCommandLine \
    -S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \
    -S ${SV_DIR}/qscript/SVQScript.q \
    -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
    -cp ${classpath} \
    -configFile ${SV_DIR}/conf/genstrip_parameters.txt \
    -tempDir ${SV_TMPDIR} \
    -R ${bundle}/human_g1k_v37.chr20.fasta \
    -runDirectory ${runDir} \
    -md ${runDir}/metadata \
    -jobLogDir ${runDir}/logs \
    -ploidyMapFile ${bundle}/human_g1k_v37.ploidymap.txt \
    -genderMapFile ${bundle}/sample_gender.map \
    -genomeMaskFile ${bundle}/human_g1k_v37.svmask.chr20.fasta \
    -L 20 \
    -tilingWindowSize 1000 \
    -tilingWindowOverlap 500 \
    -maximumReferenceGapLength 1000 \
    -boundaryPrecision 100 \
    -minimumRefinedLength 500 \
    -produceAuxiliaryFiles \
    -I ${bamList} \
    -jobRunner Drmaa \
    || exit 1

INFO  13:25:32,968 QGraph - Dry run completed successfully!
INFO  13:25:32,968 QGraph - Re-run with "-run" to execute the functions.
INFO  13:25:32,970 QCommandLine - Writing final jobs report...
INFO  13:25:32,970 QJobsReporter - Writing JobLogging GATKReport to file /BiO/psh/Project/SVtest/CNVDiscoveryPipeline.jobreport.txt
INFO  13:25:33,007 QCommandLine - Script completed successfully with 14 total jobs

ls -a cnv*/*
cnv_stage10/seq_20:
.  ..
cnv_stage11/seq_20:
.  ..
cnv_stage1/seq_20:
.  ..
cnv_stage2/seq_20:
.  ..
cnv_stage3/seq_20:
.  ..
cnv_stage4/seq_20:
.  ..
cnv_stage6/seq_20:
.  ..
cnv_stage7/seq_20:
.  ..
cnv_stage8/seq_20:
.  ..
cnv_stage9/seq_20:
.  ..
cnv_sentinel_files/:
. ..
cnv_stage12/:
. ..
cnv_stage5/:
. ..

Though this run was done successfully, Why don't the results exist anywhere?

How to run CNVDiscoveryPipeline in GenomeSTRiP2.0?

What is my script problem? What can I do resolve this problem?

Answer 1

[jglessnd]

You need to include -run in your command.

You probably need to include -gatkJobRunner Drmaa and -intervalList <File with "20"> too.

Once you do that, see result file here:

${runDir}​/cnv_stage12/gs_cnv.genotypes.vcf.gz