<?xml version="1.0" encoding="UTF-8"?>
<Global name="Annotations" version="1">

    <Category name="Genes">
        <Resource name="Ensembl Genes"
                  path="https://s3.amazonaws.com/igv.org.genomes/hg19/ensGene.txt.gz">
        </Resource>
        <Resource name="UCSC Genes" hyperlink="http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=knownGene"
                  path="http://www.broadinstitute.org/igvdata/annotations/hg19/UCSCGenes.ucscGene">
        </Resource>
        <Resource name="MGC Genes" path="http://www.broadinstitute.org/igvdata/annotations/hg19/MGCGenes.bed">
        </Resource>
        <Resource name="Gencode Genes (UCSC v10)"
                  path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/gencode.v10.annotation.ucscgene.gz"
                  index="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/gencode.v10.annotation.ucscgene.gz.tbi"
                  hyperlink="http://www.gencodegenes.org/">
        </Resource>
        <Resource name="Gencode Genes (v14)" trackLine="visibilitywindow:10000000"
                  path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/gencode.v14.annotation.sorted.gtf.gz"
                  index="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/gencode.v14.annotation.sorted.gtf.gz.tbi"
                  hyperlink="http://www.gencodegenes.org/">
        </Resource>
        <Resource name="Gencode Genes (v15)" trackLine="visibilitywindow:10000000"
                  path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/gencode.v15.annotation.sorted.gtf.gz"
                  index="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/gencode.v15.annotation.sorted.gtf.gz.tbi"
                  hyperlink="http://www.gencodegenes.org/">
        </Resource>
        <Resource name="Gencode Genes (v16)" trackLine="visibilitywindow:10000000"
                  path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/gencode.v16.annotation.sorted.gtf.gz"
                  index="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/gencode.v16.annotation.sorted.gtf.gz.tbi"
                  hyperlink="http://www.gencodegenes.org/">
        </Resource>
        <Resource name="Gencode Genes (v17)" trackLine="visibilitywindow:10000000"
                  path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/gencode.v17.annotation.sorted.gtf.gz"
                  index="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/gencode.v17.annotation.sorted.gtf.gz.tbi"
                  hyperlink="http://www.gencodegenes.org/">
        </Resource>
        <Resource name="Gencode Genes (v18)" trackLine="visibilitywindow:10000000"
                  path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/gencode.v18.annotation.sorted.gtf.gz"
                  index="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/gencode.v18.annotation.sorted.gtf.gz.tbi"
                  hyperlink="http://www.gencodegenes.org/">
        </Resource>
    </Category>
    <Category name="Phenotype and Disease Associations">
        <!--<Resource name="COSMIC" resourceType="das" hyperlink="http://www.sanger.ac.uk/genetics/CGP/cosmic/"-->
                  <!--path="http://das.sanger.ac.uk/das/cosmic_mutations_GRCh37/features"-->
                  <!--trackLine="featureVisibilityWindow=0"/>-->
        <!--<Resource name="OMIM Genes" hyperlink="https://omim.org/"-->
                  <!--url=" https://omim.org/entry/$$"-->
                  <!--path="http://www.broadinstitute.org/igvdata/annotations/hg19/phenotype/hg19_omim_genes.bed.gz"/>-->
        <Resource name="GWAS Catalog" hyperlink="http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=gwasCatalog"
                  url="http://genome.ucsc.edu/cgi-bin/hgc?g=gwasCatalog&amp;i=$$"
                  path="http://www.broadinstitute.org/igvdata/annotations/hg19/phenotype/hg19_gwas_genes.bed.gz"/>
        <Resource name="RGD Human QTL" hyperlink="http://rgd.mcw.edu/wg/home"
                  url="http://genome.ucsc.edu/cgi-bin/hgc?g=rgdQtl&amp;i=$$"
                  path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/phenotype/RGD_QTL_hg18.bed"/>


    </Category>

    <Category name="Sequence and Regulation">
        <Resource name="CpG Islands"
                  hyperlink="http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=cpgIslandExt"
                  path="http://www.broadinstitute.org/igvdata/annotations/hg19/cpgIslands.hg19.bed">
        </Resource>
        <Resource name="GC Percentage" path="http://www.broadinstitute.org/igvdata/annotations/hg19/hg19.gc5base.tdf">
        </Resource>
    </Category>

    <Category name="Variation and Repeats">
        <!--<Resource name="dbSNP 1.3.1"-->
                  <!--url="https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$$"-->
                  <!--path="http://www.broadinstitute.org/igvdata/annotations/hg19/dbSnp/hg19_snp131.bed"/>-->
        <!--<Resource name="dbSNP 1.3.7"-->
                  <!--url="https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$$"-->
                  <!--path="http://www.broadinstitute.org/igvdata/annotations/hg19/dbSnp/snp137.hg19.bed.gz"/>-->
        <Resource name="dbSNP 1.4.7"
                  url="https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$$"
                  path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/snp147.hg19.ucscsnp.gz"
                  index="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/snp147.hg19.ucscsnp.gz.tbi"/>
        <Resource name="Genomic Structural Variation (DGV)"  trackline='itemRgb="On"'
                  path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/dgv.bed.gz"
                  hyperlink="http://projects.tcag.ca/variation/"
                  url="http://genome.ucsc.edu/cgi-bin/hgc?g=dgv&amp;i=$$"/>

        <Category name="Repeat Masker" hyperlink="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&amp;g=rmsk">
            <Resource name="SINE"
                      path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/SINE.rmask.gz"
                      index="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/SINE.rmask.gz.tbi"/>
            <Resource name="LINE"
                      path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/LINE.rmask.gz"
                      index="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/LINE.rmask.gz.tbi"/>
            <Resource name="LTR"
                      path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/LTR.rmask.gz"
                      index="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/LTR.rmask.gz"/>
            <Resource name="DNA"
                      path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/DNA.rmask.gz"
                      index="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/DNA.rmask.gz.tbi"/>
            <Resource name="Simple"
                      path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/Simple_repeat.rmask.gz"
                      index="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/Simple_repeat.rmask.gz.tbi"/>
            <Resource name="Low Complexity"
                      path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/Low_complexity.rmask.gz"
                      index="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/Low_complexity.rmask.gz.tbi"/>
            <Resource name="Satellite"
                      path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/Satellite.rmask.gz"
                      index="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/Satellite.rmask.gz.tbi"/>
            <Resource name="RC"
                      path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/RC.rmask.gz"
                      index="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/RC.rmask.gz.tbi"/>
            <Resource name="RNA"
                      path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/RNA.rmask.gz"
                      index="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/RNA.rmask.gz.tbi"/>
            <!--
<Resource name="rRNA"
                      path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/rRNA.rmask.gz"/>
            <Resource name="scRNA"
                      path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/scRNA.rmask.gz"/>
            <Resource name="snRNA"
                      path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/snRNA.rmask.gz"/>
            <Resource name="srpRNA"
                      path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/srpRNA.rmask.gz"/>
            <Resource name="tRNA"
                      path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/tRNA.rmask.gz"/>
 -->
            <Resource name="Other"
                      path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/Other.rmask.gz"
                      index="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/Other.rmask.gz.tbi"/>
            <Resource name="Unknown"
                      path="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/Unknown.rmask.gz"
                      index="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/Unknown.rmask.gz/tbi"/>
        </Category>
    </Category>

    <Category name="Comparative Genomics">
        <Resource name="siphy rate (10 mer)" path="http://www.broadinstitute.org/igvdata/hg19/omega.10mers.wig.tdf"
                  hyperlink="http://bioinformatics.oxfordjournals.org/cgi/content/full/25/12/i54"/>
        <Resource name="siphy pi" path="http://www.broadinstitute.org/igvdata/hg19/pi.ewig.tdf"
                  hyperlink="http://bioinformatics.oxfordjournals.org/cgi/content/full/25/12/i54"/>
        <Resource name="Phastcons (Verterbrate 46 way)"
                  path="http://www.broadinstitute.org/igvdata/annotations/hg19/conservation/hg19_phastcon46.tdf"
                  hyperlink="http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=cons46way"/>
        <Resource name="phlyoP (Verterbrate 46 way)"
                  path="http://www.broadinstitute.org/igvdata/annotations/hg19/conservation/hg19_phyloP46way.tdf"
                  hyperlink="http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=cons46way"/>
        <Resource name="Multiple Alignments (multiz, 44 species)"
                  path="http://www.broadinstitute.org/igvdata/hg19/maf/hg19.maf.dict"
                  hyperlink="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&amp;g=cons44way">
        </Resource>
    </Category>

</Global>
