PlotGenome

use:

Default also looks for <varscan.called>.homdels so enable the homdels output

• perl $0 -d <human.dict> <varscan.called>

By region

• perl $0 -d <human.dict> -r 1,1,1000000 <varscan.called>

Also plot f/z vals:

• perl $0 -d <human.dict> <varscan.called> <vcf.table>

note: actual use example

{GATK best practices alignment using BWA}

samtools mpileup \
-R -q 40 -f human_g1k_v37.fasta Normal.human_g1k_v37.merged.bam Tumor.human_g1k_v37.merged.bam | \
java -Xmx2g -jar ${HOME}/software/VarScan.v2.3.2/VarScan.v2.3.2.jar copynumber \
- tumor --mpileup --min-segment-size 200 --max-segment-size 500;
java -jar -Xmx2g -jar ${HOME}/software/VarScan.v2.3.2/VarScan.v2.3.2.jar copyCaller \
tumor.copynumber --output-file tumor.called;
perl PlotFloatsOnInterVals0.0.3.pl -v Snps.GatkVariantsToTable.table tumor.called > tumor.called.Rscript;
Rscript tumor.called.Rscript ;


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Prereqisites

• VCF file: calculate F values with script in perlIncludeVcf.pm repository
• Varscan analysis has to be performed ("http://varscan.sourceforge.net/")
• R(script) + DNAcopy library to be installed and working
  • start R and paste
  • source("http://bioconductor.org/biocLite.R");biocLite("DNAcopy")