tapestry/trio_dev_data_igv_session.xml at main · quinlan-lab/tapestry · GitHub

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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<Session genome="hg38" locus="chr1:1,989,050-2,001,868" version="8">
    <Resources>
        <!-- PedMEC-phasing: phased VCF -->
        <Resource path="http://localhost:8000/output/pedmec-phasing/CEPH-1463.joint.GRCh38.deepvariant.glnexus.phased.vcf.gz" type="vcf"/>
        <!-- PedMEC-phasing: phase blocks (GTF) -->
        <Resource path="http://localhost:8000/output/pedmec-phasing/CEPH-1463.joint.GRCh38.deepvariant.glnexus.phased.NA12878.blocks.gtf" type="gtf"/>
        <Resource path="http://localhost:8000/output/pedmec-phasing/CEPH-1463.joint.GRCh38.deepvariant.glnexus.phased.NA12891.blocks.gtf" type="gtf"/>
        <Resource path="http://localhost:8000/output/pedmec-phasing/CEPH-1463.joint.GRCh38.deepvariant.glnexus.phased.NA12892.blocks.gtf" type="gtf"/>
        <!-- PedMEC-phasing: haplotagged BAMs -->
        <Resource path="http://localhost:8000/output/pedmec-phasing/NA12878.GRCh38.haplotagged.bam" type="bam"/>
        <Resource path="http://localhost:8000/output/pedmec-phasing/NA12891.GRCh38.haplotagged.bam" type="bam"/>
        <Resource path="http://localhost:8000/output/pedmec-phasing/NA12892.GRCh38.haplotagged.bam" type="bam"/>
        <!-- Kid methylation bigwigs -->
        <Resource path="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased.all-cpgs/NA12878.dna-methylation.combined.count.hg38.bw"/>
        <Resource path="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12878.dna-methylation.pat.count.hg38.bw"/>
        <Resource path="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12878.dna-methylation.mat.count.hg38.bw"/>
        <!-- Dad methylation bigwigs -->
        <Resource path="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased.all-cpgs/NA12891.dna-methylation.combined.count.hg38.bw"/>
        <Resource path="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12891.dna-methylation.A.count.hg38.bw"/>
        <Resource path="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12891.dna-methylation.B.count.hg38.bw"/>
        <!-- Mom methylation bigwigs -->
        <Resource path="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased.all-cpgs/NA12892.dna-methylation.combined.count.hg38.bw"/>
        <Resource path="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12892.dna-methylation.C.count.hg38.bw"/>
        <Resource path="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12892.dna-methylation.D.count.hg38.bw"/>
        <!-- Parent-phased: kid hap-map blocks -->
        <Resource path="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12878.hap-map-blocks.paternal.sorted.bed.gz"/>
        <Resource path="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12878.hap-map-blocks.maternal.sorted.bed.gz"/>
        <!-- Parent-phased: kid bit-vector mismatch sites -->
        <Resource path="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12878.bit-vector-sites-mismatches.paternal.vcf.gz" type="vcf"/>
        <Resource path="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12878.bit-vector-sites-mismatches.maternal.vcf.gz" type="vcf"/>
    </Resources>
    <!-- Phased VCF -->
    <Panel height="150" name="DataPanel" width="2163">
        <Track attributeKey="CEPH-1463.joint.GRCh38.deepvariant.glnexus.phased.vcf.gz" clazz="org.broad.igv.variant.VariantTrack" displayMode="EXPANDED" fontSize="10" id="http://localhost:8000/output/pedmec-phasing/CEPH-1463.joint.GRCh38.deepvariant.glnexus.phased.vcf.gz" name="CEPH-1463.joint.GRCh38.deepvariant.glnexus.phased.vcf.gz" siteColorMode="ALLELE_FREQUENCY" visible="true"/>
    </Panel>
    <!-- Kid (NA12878): BAM + methylation bigwigs + hap-map blocks -->
    <Panel height="500" name="PanelKid" width="2163">
        <Track attributeKey="NA12878.GRCh38.haplotagged.bam Coverage" clazz="org.broad.igv.sam.CoverageTrack" fontSize="10" id="http://localhost:8000/output/pedmec-phasing/NA12878.GRCh38.haplotagged.bam_coverage" name="NA12878 Coverage" visible="false"/>
        <Track attributeKey="NA12878.GRCh38.haplotagged.bam" clazz="org.broad.igv.sam.AlignmentTrack" color="185,185,185" displayMode="SQUISHED" experimentType="THIRD_GEN" fontSize="10" height="150" id="http://localhost:8000/output/pedmec-phasing/NA12878.GRCh38.haplotagged.bam" name="NA12878 BAM" visible="true">
            <RenderOptions colorByTag="PS" colorOption="TAG" groupByOption="PHASE" hideSmallIndels="true" smallIndelThreshold="100"/>
        </Track>
        <Track attributeKey="NA12878.dna-methylation.combined.count.hg38.bw" autoScale="false" clazz="org.broad.igv.track.DataSourceTrack" fontSize="10" id="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased.all-cpgs/NA12878.dna-methylation.combined.count.hg38.bw" name="NA12878 count-meth combined" renderer="BAR_CHART" visible="true" color="0,128,0">
            <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="1.0" minimum="0.0" type="LINEAR"/>
        </Track>
        <Track attributeKey="NA12878.dna-methylation.pat.count.hg38.bw" autoScale="false" clazz="org.broad.igv.track.DataSourceTrack" fontSize="10" id="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12878.dna-methylation.pat.count.hg38.bw" name="NA12878 count-meth pat" renderer="BAR_CHART" visible="true" color="0,0,255">
            <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="1.0" minimum="0.0" type="LINEAR"/>
        </Track>
        <Track attributeKey="NA12878.dna-methylation.mat.count.hg38.bw" autoScale="false" clazz="org.broad.igv.track.DataSourceTrack" fontSize="10" id="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12878.dna-methylation.mat.count.hg38.bw" name="NA12878 count-meth mat" renderer="BAR_CHART" visible="true" color="255,0,0">
            <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="1.0" minimum="0.0" type="LINEAR"/>
        </Track>
        <Track attributeKey="NA12878.hap-map-blocks.paternal.sorted.bed.gz" clazz="org.broad.igv.track.FeatureTrack" fontSize="10" id="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12878.hap-map-blocks.paternal.sorted.bed.gz" name="NA12878 hap-map blks pat" visible="true"/>
        <Track attributeKey="NA12878.hap-map-blocks.maternal.sorted.bed.gz" clazz="org.broad.igv.track.FeatureTrack" fontSize="10" id="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12878.hap-map-blocks.maternal.sorted.bed.gz" name="NA12878 hap-map blks mat" visible="true"/>
        <Track attributeKey="NA12878.bit-vector-sites-mismatches.paternal.vcf.gz" clazz="org.broad.igv.variant.VariantTrack" displayMode="COLLAPSED" fontSize="10" id="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12878.bit-vector-sites-mismatches.paternal.vcf.gz" name="NA12878 bitvec mismatch pat" visible="true" showGenotypes="false"/>
        <Track attributeKey="NA12878.bit-vector-sites-mismatches.maternal.vcf.gz" clazz="org.broad.igv.variant.VariantTrack" displayMode="COLLAPSED" fontSize="10" id="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12878.bit-vector-sites-mismatches.maternal.vcf.gz" name="NA12878 bitvec mismatch mat" visible="true" showGenotypes="false"/>
    </Panel>
    <!-- Dad (NA12891): BAM + methylation bigwigs -->
    <Panel height="350" name="PanelDad" width="2163">
        <Track attributeKey="NA12891.GRCh38.haplotagged.bam Coverage" clazz="org.broad.igv.sam.CoverageTrack" fontSize="10" id="http://localhost:8000/output/pedmec-phasing/NA12891.GRCh38.haplotagged.bam_coverage" name="NA12891 Coverage" visible="false"/>
        <Track attributeKey="NA12891.GRCh38.haplotagged.bam" clazz="org.broad.igv.sam.AlignmentTrack" color="185,185,185" displayMode="SQUISHED" experimentType="THIRD_GEN" fontSize="10" height="150" id="http://localhost:8000/output/pedmec-phasing/NA12891.GRCh38.haplotagged.bam" name="NA12891 BAM" visible="true">
            <RenderOptions colorByTag="PS" colorOption="TAG" groupByOption="PHASE" hideSmallIndels="true" smallIndelThreshold="100"/>
        </Track>
        <Track attributeKey="NA12891.dna-methylation.combined.count.hg38.bw" autoScale="false" clazz="org.broad.igv.track.DataSourceTrack" fontSize="10" id="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased.all-cpgs/NA12891.dna-methylation.combined.count.hg38.bw" name="NA12891 count-meth combined" renderer="BAR_CHART" visible="true" color="0,128,0">
            <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="1.0" minimum="0.0" type="LINEAR"/>
        </Track>
        <Track attributeKey="NA12891.dna-methylation.A.count.hg38.bw" autoScale="false" clazz="org.broad.igv.track.DataSourceTrack" fontSize="10" id="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12891.dna-methylation.A.count.hg38.bw" name="NA12891 count-meth A" renderer="BAR_CHART" visible="true" color="0,0,255">
            <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="1.0" minimum="0.0" type="LINEAR"/>
        </Track>
        <Track attributeKey="NA12891.dna-methylation.B.count.hg38.bw" autoScale="false" clazz="org.broad.igv.track.DataSourceTrack" fontSize="10" id="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12891.dna-methylation.B.count.hg38.bw" name="NA12891 count-meth B" renderer="BAR_CHART" visible="true" color="255,0,0">
            <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="1.0" minimum="0.0" type="LINEAR"/>
        </Track>
    </Panel>
    <!-- Mom (NA12892): BAM + methylation bigwigs -->
    <Panel height="350" name="PanelMom" width="2163">
        <Track attributeKey="NA12892.GRCh38.haplotagged.bam Coverage" clazz="org.broad.igv.sam.CoverageTrack" fontSize="10" id="http://localhost:8000/output/pedmec-phasing/NA12892.GRCh38.haplotagged.bam_coverage" name="NA12892 Coverage" visible="false"/>
        <Track attributeKey="NA12892.GRCh38.haplotagged.bam" clazz="org.broad.igv.sam.AlignmentTrack" color="185,185,185" displayMode="SQUISHED" experimentType="THIRD_GEN" fontSize="10" height="150" id="http://localhost:8000/output/pedmec-phasing/NA12892.GRCh38.haplotagged.bam" name="NA12892 BAM" visible="true">
            <RenderOptions colorByTag="PS" colorOption="TAG" groupByOption="PHASE" hideSmallIndels="true" smallIndelThreshold="100"/>
        </Track>
        <Track attributeKey="NA12892.dna-methylation.combined.count.hg38.bw" autoScale="false" clazz="org.broad.igv.track.DataSourceTrack" fontSize="10" id="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased.all-cpgs/NA12892.dna-methylation.combined.count.hg38.bw" name="NA12892 count-meth combined" renderer="BAR_CHART" visible="true" color="0,128,0">
            <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="1.0" minimum="0.0" type="LINEAR"/>
        </Track>
        <Track attributeKey="NA12892.dna-methylation.C.count.hg38.bw" autoScale="false" clazz="org.broad.igv.track.DataSourceTrack" fontSize="10" id="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12892.dna-methylation.C.count.hg38.bw" name="NA12892 count-meth C" renderer="BAR_CHART" visible="true" color="0,0,255">
            <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="1.0" minimum="0.0" type="LINEAR"/>
        </Track>
        <Track attributeKey="NA12892.dna-methylation.D.count.hg38.bw" autoScale="false" clazz="org.broad.igv.track.DataSourceTrack" fontSize="10" id="http://localhost:8000/output/dna-methylation/CEPH1463.GRCh38.hifi.parent-phased/NA12892.dna-methylation.D.count.hg38.bw" name="NA12892 count-meth D" renderer="BAR_CHART" visible="true" color="255,0,0">
            <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="1.0" minimum="0.0" type="LINEAR"/>
        </Track>
    </Panel>
    <!-- Feature panel: phase blocks + reference -->
    <Panel height="200" name="FeaturePanel" width="2163">
        <Track attributeKey="Reference sequence" clazz="org.broad.igv.track.SequenceTrack" fontSize="10" id="Reference sequence" name="Reference sequence" sequenceTranslationStrandValue="+" shouldShowTranslation="false" visible="true"/>
        <Track attributeKey="CEPH-1463.joint.GRCh38.deepvariant.glnexus.phased.NA12878.blocks.gtf" clazz="org.broad.igv.track.FeatureTrack" fontSize="10" id="http://localhost:8000/output/pedmec-phasing/CEPH-1463.joint.GRCh38.deepvariant.glnexus.phased.NA12878.blocks.gtf" name="NA12878 phase blocks" visible="true"/>
        <Track attributeKey="CEPH-1463.joint.GRCh38.deepvariant.glnexus.phased.NA12891.blocks.gtf" clazz="org.broad.igv.track.FeatureTrack" fontSize="10" id="http://localhost:8000/output/pedmec-phasing/CEPH-1463.joint.GRCh38.deepvariant.glnexus.phased.NA12891.blocks.gtf" name="NA12891 phase blocks" visible="true"/>
        <Track attributeKey="CEPH-1463.joint.GRCh38.deepvariant.glnexus.phased.NA12892.blocks.gtf" clazz="org.broad.igv.track.FeatureTrack" fontSize="10" id="http://localhost:8000/output/pedmec-phasing/CEPH-1463.joint.GRCh38.deepvariant.glnexus.phased.NA12892.blocks.gtf" name="NA12892 phase blocks" visible="true"/>
    </Panel>
    <HiddenAttributes>
        <Attribute name="DATA FILE"/>
        <Attribute name="DATA TYPE"/>
        <Attribute name="NAME"/>
    </HiddenAttributes>
</Session>