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I need some tips to run GenomeSTRiP - CNVDiscovery

Hi,
I'm trying to call CNVs by GenomeSTRiP software.
As I know, I should run SVpreprocess first and CNVDiscovery second.
So I tried SVpreprocess but It won't work.
The errer said they need more option "-ploidyMapFile" even I only put autosome.
Is it essential to call CNVs from only autosome?
then how can i get the file? I'm working on pig data..

And if my process was wrong, or whatever, I want to know the exact process(or cord) to call CNVs..

(+)

!/bin/bash

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

SVpreprocess

java -Xmx40g -cp ${classpath} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/SVPreprocess.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-cp ${classpath} \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-R Ref/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa \
-I DURvsKWB.bam.list \
-md mdtest/ \
-bamFilesAreDisjoint true \
-jobLogDir CNVtest/logDir2 \
-run

CNVDiscovery

java -Xmx40g -cp ${classpath} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-cp ${classpath} \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-R Ref/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa \
-I DURvsKWB.bam.list \
-genderMapFile DURvsKWB.gender.txt \
-md mdtest/ \
-runDirectory CNVtest/ \
-jobLogDir CNVtest/log \
-intervalList chr.list \
-tilingWindowSize 1000 \
-tilingWindowOverlap 500 \
-maximumReferenceGapLength 1000 \
-boundaryPrecision 100 \
-minimumRefinedLength 500 \
-run

I attached the cord i used.

Answers

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