diff --git a/python/gatherIndelsToVCF.py b/python/gatherIndelsToVCF.py
new file mode 100755
index 000000000..3a2a45a19
--- /dev/null
+++ b/python/gatherIndelsToVCF.py
@@ -0,0 +1,231 @@
+#!/usr/bin/env python
+
+import os
+import sys
+
+input_verbose_beds = sys.argv[1].split(",")
+output_vcf_name = sys.argv[2]
+reference_file = sys.argv[3]
+
+vcf_header = ["#CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"]
+format = "GT:FT"
+class Indel:
+    def __init__(self,chrom,start,stop,bases,sample,isHet,isDeletion,isFiltered,isCoding,
+                 consF,consR,refF,refR,consMM,refMM):
+        self.chrom = chrom
+        self.start = start
+        self.stop = stop
+        self.bases = bases
+        self.isDeletion = isDeletion
+        self.isFiltered = isFiltered
+        self.isHet = isHet
+        self.sample = sample
+        self.isCoding = isCoding
+        self.consForward = int(consF)
+        self.consReverse = int(consR)
+        self.refForward = int(refF)
+        self.refReverse = int(refR)
+        self.consMM = float(consMM)
+        self.refMM = float(refMM)
+
+    def getAnnotations__DO_NOT_USE(self):
+        ## note: log(1/2) ~~ -0.3
+        forwardLod = -0.3*(self.consForward+self.refForward) + 2*self.consForward
+        reverseLod = -0.3*(self.consReverse+self.refReverse) + 2*self.consReverse
+        totalLod = -0.3*(self.consForward+self.consReverse+self.refForward+self.refReverse) + 2*(self.consForward+self.consReverse)
+        strand_score = max(forwardLod-totalLod,reverseLod-totalLod)
+        SB = "SB="+str(strand_score)
+        mismatch = "MMR="+str(self.consMM)
+        ref_mismatch = "refMMR="+str(self.refMM)
+        return [SB,mismatch,ref_mismatch]
+
+    def getTotalLod(self):
+        return -0.3*(self.consForward+self.consReverse+self.refForward+self.refReverse) + 2*(self.consForward+self.consReverse)
+
+    def getFwdLod(self):
+        return -0.3*(self.consForward+self.refForward) + 2*self.consForward
+
+    def getRevLod(self):
+        return -0.3*(self.consReverse+self.refReverse) + 2*self.consReverse
+
+def getAnnotations(indelList):
+    total_lod = 0.0
+    total_fwd_lod = 0.0
+    total_rev_lod = 0.0
+    avg_mmr = 0.0
+    avg_ref_mmr = 0.0
+    for indel in indelList:
+        total_lod += indel.getTotalLod()
+        total_fwd_lod += indel.getFwdLod()
+        total_rev_lod += indel.getRevLod()
+        avg_mmr += indel.consMM
+        avg_ref_mmr += indel.refMM
+    avg_mmr = avg_mmr/len(indelList)
+    avg_ref_mmr = avg_ref_mmr/len(indelList)
+    strand_score = max(total_fwd_lod-total_lod,total_rev_lod-total_lod)
+    SB = "SB="+str(strand_score)
+    mismatch = "MMR="+str(avg_mmr)
+    ref_mismatch = "refMMR="+str(avg_ref_mmr)
+    return [SB,mismatch,ref_mismatch]
+
+def getGenotypes(samples,indels,alts):
+    s2i = dict()
+    alts = alts.split(",")
+    genotypes = list()
+    for indel in indels:
+        s2i[indel.sample] = indel
+    for sample in samples:
+        if ( sample in s2i.keys() ):
+            if ( s2i[sample].isDeletion ):
+                bases = "D"+str(s2i[sample].bases)
+            else:
+                bases = "I"+s2i[sample].bases
+            gt_index = str(1+alts.index(bases))
+            if ( s2i[sample].isHet ):
+                gtstr = "0/"+gt_index
+            else:
+                gtstr = gt_index+"/"+gt_index
+            if ( s2i[sample].isFiltered ):
+                gtstr += ":1"
+            else:
+                gtstr += ":0"
+        else:
+            gtstr = "0/0:0"
+        genotypes.append(gtstr)
+    return genotypes            
+
+def getAlts(indel_list):
+    alts = list()
+    for indel in indel_list:
+        if ( indel.isDeletion ):
+            if ( not "D"+indel.bases in alts ):
+                alts.append("D"+indel.bases)
+        else:
+            if ( not "I"+indel.bases in alts ):
+                alts.append("I"+indel.bases)
+                
+    alt = ",".join(alts)
+
+    return alt
+
+def fixAlts(alts_in):
+    alts = alts_in.split(",")
+    fixed_alts = list()
+    for alt in alts:
+        if ( alt.startswith("D") ):
+            fixed_alts.append("D"+str(len(alt)-1))
+        else:
+            fixed_alts.append(alt)
+    return ",".join(fixed_alts)
+
+def fixChrom(chrom):
+    if ( chrom == "23" ):
+        return "X"
+    if ( chrom == "24" ):
+        return "Y"
+    return chrom
+
+def writeVCFLine(out_stream,indel_list,sample_list):
+    alts = getAlts(indel_list)
+    ID = "." ## ignore dbsnp annotation for now
+    chrom = str(indel_list[0].chrom)
+    start = str(indel_list[0].start)
+    if ( indel_list[0].isCoding ):
+        info = "type=Codon;"
+    else:
+        info = "type=Intron;"
+    info += "count="+str(len(indel_list))
+    # format is global
+    def inSampleOrdering(indel1,indel2):
+        return sample_list.index(indel1.sample)-sample_list.index(indel2.sample)
+    indel_list.sort(inSampleOrdering)
+    fixed_alts = fixAlts(alts)
+    if ( True or not fixed_alts.find(",") > -1 ):
+        info += ";"+";".join(getAnnotations(indel_list))
+    entries = [fixChrom(chrom),start,ID,"A",fixed_alts,"50","0",info,format]
+    for e in getGenotypes(sample_list,indel_list,alts):
+        entries.append(e)
+    out_stream.write("\t".join(entries)+"\n")
+
+def startCompare(ind1,ind2):
+    if ( ind1.chrom != ind2.chrom ):
+        return ind1.chrom - ind2.chrom
+    else:
+        return ind1.start - ind2.start
+
+def output(indels,popname,samples):
+    outfile = open(output_vcf_name+"_BAD_REFERENCE.vcf",'w')
+    outfile.write("##VCFv3.2\n##Created by gatherIndelsToVCF.py\n")
+    outfile.write("\t".join(vcf_header)+"\t"+"\t".join(samples)+"\n")
+    indels_for_line = list()
+    for indel in indels:
+        if ( len(indels_for_line) == 0 or startCompare(indel,indels_for_line[len(indels_for_line)-1]) == 0 ):
+            indels_for_line.append(indel)
+        else:
+            writeVCFLine(outfile,indels_for_line,samples)
+            indels_for_line = list()
+    outfile.close()
+
+def parseSample(filename):
+    return filename.split(".",1)[0]
+
+def parseIndels(filePath,sampleName):
+    f = open(filePath)
+    indels = list()
+    for line in f.readlines():
+        if ( not line.startswith("[") ):
+            spline = line.split("\t")
+            if ( spline[0] != "X" and spline[0] != "Y" ):
+                chrom = int(spline[0])
+            else:
+                if ( spline[0] == "X"):
+                    chrom = 23
+                else:
+                    chrom = 24
+            start = int(spline[1])
+            stop = int(spline[2])
+            rawbase = spline[3]
+            isDeletion = rawbase.startswith("-")
+            if ( isDeletion ):
+                bases = spline[3].split("-")[1]
+            else:
+                bases = spline[3].split("+")[1]
+            sample = sampleName
+            isFiltered = False
+            if ( line.find("AUTOFILTER") > -1 ):
+                if ( line.find("CONS_AV_MM") > -1 ):
+                    mm = float(line.split("AV_MM[C/R]:")[1].split("/")[0])
+                    if ( mm >= 3.5 ):
+                        isFiltered = True
+                else:
+                    isFiltered = True
+            isCoding = line.find("CODING") > -1
+            isHet = True ## haven't seen a hom yet---todo --- fix this
+            # STRAND_COUNTS[C/C/R/R]:
+            strand_counts_field = line.split("STRAND_COUNTS[C/C/R/R]:")[1].split()[0]
+            strand_counts = strand_counts_field.split("/")
+            consF = strand_counts[0]
+            consR = strand_counts[1]
+            refF = strand_counts[2]
+            refR = strand_counts[3]
+            # AV_MM[C/R]:
+            mismatch_field = line.split("AV_MM[C/R]:")[1].split()[0]
+            consMM = mismatch_field.split("/")[0]
+            refMM = mismatch_field.split("/")[1]
+            # recall order: self,chrom,start,stop,bases,sample,isHet,isDeletion,isFiltered,isCoding
+            indels.append(Indel(chrom,start,stop,bases,sample,isHet,isDeletion,isFiltered,isCoding,consF,consR,refF,refR,consMM,refMM))
+    return indels
+
+def writeVCF(verbose_bed_list):
+    for file in verbose_bed_list:
+        samples.append(parseSample(file))
+        indels.extend(parseIndels(indel_dir+file,parseSample(file)))
+    indels.sort(startCompare)
+    output(indels,popname,samples)
+
+writeVCF(input_verbose_beds)
+
+## now dumb hacky thing
+
+cmd = "java -jar /humgen/gsa-scr1/chartl/sting/dist/GenomeAnalysisTK.jar -T VCFReferenceFixer -B fixme,VCF,"+output_vcf_name+"_BAD_REFERENCE.vcf -o "+output_vcf_name+" -R "+reference_file+" -l INFO"
+os.system(cmd)