Scripts for personal use

Script list

boxplot.R -- Boxplot for different size of data
fetch_sig_pairs.pl -- Fetch significant gene pairs from a correlation matrix in csv format
getCenteredSig.pl -- Prepare the heatmap around the peak center
run_refinement.pl -- A pipeline for running GATK (makdup, realignment, recalibration)
mergeSamtoolsFlagstatResult.pl -- Read a fold containing "samtools flagstat" outputs and merge them together

Name		Name	Last commit message	Last commit date
Latest commit History 22 Commits
cnv		cnv
vcfCluster		vcfCluster
GapintersetBed.pl		GapintersetBed.pl
README.md		README.md
addSNPID.pl		addSNPID.pl
annotatePeaks.pl		annotatePeaks.pl
annotation_conifer_calls.cnv.pl		annotation_conifer_calls.cnv.pl
annovaReAnno.pl		annovaReAnno.pl
annovaReAnnoHash.pl		annovaReAnnoHash.pl
bam2count.R		bam2count.R
bammapped		bammapped
bed2count.R		bed2count.R
boxplot.R		boxplot.R
callSNPsFromBase.pl		callSNPsFromBase.pl
fa2individalfa.pl		fa2individalfa.pl
fetch_sig_pairs.pl		fetch_sig_pairs.pl
getCenteredSig.pl		getCenteredSig.pl
getCenteredSigStrand.pl		getCenteredSigStrand.pl
getFunctional.pl		getFunctional.pl
makeTracks.pl		makeTracks.pl
mergeSamtoolsFlagstatResult.pl		mergeSamtoolsFlagstatResult.pl
merge_fpkm.pl		merge_fpkm.pl
peakToNearstPeak.pl		peakToNearstPeak.pl
run_refinement.pl		run_refinement.pl
vcf2SIFT.pl		vcf2SIFT.pl