To use this module, you'll first have to take your VCF and create an R-readable table out of it with the following command:
python /path/to/Sting/trunk/python/vcf2table.py -f CHROM,POS,ID,AC,AF,AN,DB,DP,HRun,MQ,MQ0,MyHaplotypeScore,QD,SB my.vcf > my.vcf.table
Then, simply invoke this module with the command:
Rscript /path/to/Sting/trunk/R/VariantRecalibratorReport/VariantRecalibratorReport.R /path/to/output/prefix /path/to/my/my.clusters /path/to/my.vcf.table [/path/to/my.suspicious.loci]
This will create a number of plots all with the prefix "/path/to/output/prefix". For instance, if you used QD, SB, HRun, and MyHaplotypeScore annotations during clustering, you should see output like this:
/path/to/output/prefix.anndist.HRun.pdf
/path/to/output/prefix.anndist.MyHaplotypeScore.pdf
/path/to/output/prefix.anndist.QD.pdf
/path/to/output/prefix.anndist.SB.pdf
/path/to/output/prefix.cluster.HRun_vs_MyHaplotypeScore.pdf
/path/to/output/prefix.cluster.HRun_vs_QD.pdf
/path/to/output/prefix.cluster.HRun_vs_SB.pdf
/path/to/output/prefix.cluster.MyHaplotypeScore_vs_HRun.pdf
/path/to/output/prefix.cluster.MyHaplotypeScore_vs_QD.pdf
/path/to/output/prefix.cluster.MyHaplotypeScore_vs_SB.pdf
/path/to/output/prefix.cluster.QD_vs_HRun.pdf
/path/to/output/prefix.cluster.QD_vs_MyHaplotypeScore.pdf
/path/to/output/prefix.cluster.QD_vs_SB.pdf
/path/to/output/prefix.cluster.SB_vs_HRun.pdf
/path/to/output/prefix.cluster.SB_vs_MyHaplotypeScore.pdf
/path/to/output/prefix.cluster.SB_vs_QD.pdf
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3936 348d0f76-0448-11de-a6fe-93d51630548a
depristo
kiran