Repository 'cnv_vcf2json'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/cnv_vcf2json

Changeset 0:c8caf812d33b (2024-03-01)
Next changeset 1:7d2d2e3b9891 (2024-07-24)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json commit 485fd56c701872217e6d6ccc4321c1f0522ad540
added:
cnv-vcf2json.xml
macros.xml
test-data/HG00096.cnv.vcf
test-data/output.json
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diff -r 000000000000 -r c8caf812d33b cnv-vcf2json.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cnv-vcf2json.xml Fri Mar 01 07:19:35 2024 +0000
[
@@ -0,0 +1,31 @@
+<tool id="cnv_vcf2json" name="CNV VCF2JSON" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Converts 1000hg structural variants VCF file to JSON</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="creators"/>
+    <command detect_errors="exit_code"><![CDATA[   
+        #import re
+        ln -s '$input_vcf_file' ./input.vcf &&
+        cnv-vcf2json
+            -i ./input.vcf
+            -o output.json
+    ]]></command>
+    <inputs>
+        <param name="input_vcf_file" type="data" format="vcf" label="CNV VCF file" help="" />
+    </inputs>
+    <outputs>
+        <data name="output_json" format="json" label="${tool.name} on ${on_string}: CNV JSON File" from_work_dir="output.json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_vcf_file" ftype="vcf" value="HG00096.cnv.vcf" />
+            <output name="output_json" file="output.json" />
+        </test>
+    </tests>
+    <help><![CDATA[
+         The tool converts the structural variants VCF file into JSON file as a preprocessing step to import the data into Beacon2 MongoDB protocol
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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diff -r 000000000000 -r c8caf812d33b macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Mar 01 07:19:35 2024 +0000
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@@ -0,0 +1,26 @@
+<macros>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@TOOL_VERSION@">1.0.4</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">cnv-vcf2json</requirement>
+        </requirements>
+    </xml>
+    <xml name="creators">
+        <creator>
+            <person givenName="Khaled" familyName="Jum'ah" url="https://github.com/khaled196" />
+            <person givenName="Krzysztof" familyName="Poterlowicz" url="https://github.com/poterlowicz-lab" />
+            <organization name="poterlowicz-lab" url="https://github.com/poterlowicz-lab" />
+        </creator>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">@misc{cnv-vcf2json,
+    author = {Khaled Jum'ah},
+    title = {{cnv-vcf2json}: Convert VCF Files to JSON Format},
+    year = {2024},
+    version = {1.0.4},
+    url = {https://pypi.org/project/cnv-vcf2json/},}</citation>
+        </citations>
+    </xml>
+</macros>
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diff -r 000000000000 -r c8caf812d33b test-data/HG00096.cnv.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HG00096.cnv.vcf Fri Mar 01 07:19:35 2024 +0000
b
b'@@ -0,0 +1,637 @@\n+##fileformat=VCFv4.2\n+##ALT=<ID=CNV,Description="Copy number variant region">\n+##ALT=<ID=DEL,Description="Deletion relative to the reference">\n+##ALT=<ID=DUP,Description="Region of elevated copy number relative to the reference">\n+##contig=<ID=chr1,length=248956422>\n+##contig=<ID=chr2,length=242193529>\n+##contig=<ID=chr3,length=198295559>\n+##contig=<ID=chr4,length=190214555>\n+##contig=<ID=chr5,length=181538259>\n+##contig=<ID=chr6,length=170805979>\n+##contig=<ID=chr7,length=159345973>\n+##contig=<ID=chr8,length=145138636>\n+##contig=<ID=chr9,length=138394717>\n+##contig=<ID=chr10,length=133797422>\n+##contig=<ID=chr11,length=135086622>\n+##contig=<ID=chr12,length=133275309>\n+##contig=<ID=chr13,length=114364328>\n+##contig=<ID=chr14,length=107043718>\n+##contig=<ID=chr15,length=101991189>\n+##contig=<ID=chr16,length=90338345>\n+##contig=<ID=chr17,length=83257441>\n+##contig=<ID=chr18,length=80373285>\n+##contig=<ID=chr19,length=58617616>\n+##contig=<ID=chr20,length=64444167>\n+##contig=<ID=chr21,length=46709983>\n+##contig=<ID=chr22,length=50818468>\n+##contig=<ID=chrX,length=156040895>\n+##contig=<ID=chrY,length=57227415>\n+##reference=file:///ephemeral/reference/index\n+##INFO=<ID=REFLEN,Number=1,Type=Integer,Description="Number of REF positions included in this record">\n+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">\n+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">\n+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS">\n+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END">\n+##FILTER=<ID=cnvLength,Description="CNV with length below 10000">\n+##FILTER=<ID=cnvQual,Description="CNV with quality below 10">\n+##FILTER=<ID=cnvBinSupportRatio,Description="CNV with low supporting number of bins with respect to event length">\n+##FILTER=<ID=cnvCopyRatio,Description="CNV with copy ratio within +/- 0.2 of 1.0">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=SM,Number=1,Type=Float,Description="Linear copy ratio of the segment mean">\n+##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Estimated copy number">\n+##FORMAT=<ID=BC,Number=1,Type=Integer,Description="Number of bins in the region">\n+##FORMAT=<ID=PE,Number=2,Type=Integer,Description="Number of improperly paired end reads at start and stop breakpoints">\n+##DRAGENCommandLine=<ID=dragen,Date="Sun Jun 14 03:04:52 UTC 2020",CommandLineOptions="--lic-instance-id-location /opt/instance-identity --ref-dir /ephemeral/reference/index --output-directory /output/HG00096 --intermediate-results-dir /ephemeral --output-file-prefix HG00096 -f --bam-input /mount/bams/HG00096.bam --enable-cnv true --cnv-enable-self-normalization True --enable-map-align True --enable-map-align-output true --output-format BAM --enable-duplicate-marking True --repeat-genotype-enable true --autodetect-reference-validate true --enable-variant-caller true --vc-emit-ref-confidence GVCF --vc-enable-roh True --vc-enable-vcf-output True --enable-sv true --sample-sex male --lic-server https://XXXXXXXXXXXX:YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY@license.edicogenome.com">\n+##DRAGENVersion=<ID=dragen,Version="SW: 05.021.510.3.5.7b, HW: 05.021.510">\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tHG00096\n+chr1\t2650427\tDRAGEN:LOSS:chr1:2650428-2651463\tN\t<DEL>\t48\tcnvLength\tSVTYPE=CNV;END=2651463;REFLEN=1036\tGT:SM:CN:BC:PE\t1/1:1.00369e-09:0:1:51,519\n+chr1\t2651463\tDRAGEN:LOSS:chr1:2651464-2653075\tN\t<DEL>\t24\tcnvLength\tSVTYPE=CNV;END=2653075;REFLEN=1612\tGT:SM:CN:BC:PE\t0/1:0.395524:1:1:519,492\n+chr1\t4063594\tDRAGEN:LOSS:chr1:4063595-4067475\tN\t<DEL>\t30\tcnvLength\tSVTYPE=CNV;END=4067475;REFLEN=3881\tGT:SM:CN:BC:PE\t0/1:0.429788:1:3:9,24\n+chr1\t6377770\tDRAGEN:LOSS:chr1:6377771-6385660\tN\t<DEL>\t27\tcnvLength\tSVTYPE=CNV;END=6385660;REFLEN=7890\tGT:SM:CN:BC:PE\t0/1:0.543097:1:6:24,17\n+chr1\t8143311\tDRAGEN:GAIN:chr1:8143312-8150440\tN\t<DUP>\t22\tcnvLength\tSVTYPE=CNV;END=8150440;REFLEN=712'..b'EL>\t41\tPASS\tSVTYPE=CNV;END=1182671;REFLEN=16397\tGT:SM:CN:BC:PE\t0/1:0.351645:1:9:22,31\n+chrX\t5137101\tDRAGEN:LOSS:chrX:5137102-5139130\tN\t<DEL>\t54\tcnvLength\tSVTYPE=CNV;END=5139130;REFLEN=2029\tGT:SM:CN:BC:PE\t1:1.00369e-09:0:2:18,19\n+chrX\t34421912\tDRAGEN:LOSS:chrX:34421913-34424508\tN\t<DEL>\t56\tcnvLength\tSVTYPE=CNV;END=34424508;REFLEN=2596\tGT:SM:CN:BC:PE\t1:1.00369e-09:0:2:0,2\n+chrX\t57696712\tDRAGEN:LOSS:chrX:57696713-57697807\tN\t<DEL>\t46\tcnvLength\tSVTYPE=CNV;END=57697807;REFLEN=1095\tGT:SM:CN:BC:PE\t1:0.022804:0:1:0,29\n+chrX\t58488950\tDRAGEN:LOSS:chrX:58488951-58498494\tN\t<DEL>\t71\tcnvLength\tSVTYPE=CNV;END=58498494;REFLEN=9544\tGT:SM:CN:BC:PE\t1:1.00369e-09:0:5:2,13\n+chrX\t62761526\tDRAGEN:GAIN:chrX:62761527-62771085\tN\t<DUP>\t56\tcnvLength\tSVTYPE=CNV;END=62771085;REFLEN=9559\tGT:SM:CN:BC:PE\t1:1.8673:2:9:27,31\n+chrX\t75996647\tDRAGEN:GAIN:chrX:75996648-76002528\tN\t<DUP>\t54\tcnvLength\tSVTYPE=CNV;END=76002528;REFLEN=5881\tGT:SM:CN:BC:PE\t1:1.90476:2:5:0,1\n+chrX\t77865333\tDRAGEN:LOSS:chrX:77865334-77867847\tN\t<DEL>\t56\tcnvLength\tSVTYPE=CNV;END=77867847;REFLEN=2514\tGT:SM:CN:BC:PE\t1:9.70144e-06:0:2:23,16\n+chrX\t96808172\tDRAGEN:LOSS:chrX:96808173-96809172\tN\t<DEL>\t43\tcnvLength\tSVTYPE=CNV;END=96809172;REFLEN=1000\tGT:SM:CN:BC:PE\t1:0.0487332:0:1:38,32\n+chrX\t104003381\tDRAGEN:GAIN:chrX:104003382-104050640\tN\t<DUP>\t88\tPASS\tSVTYPE=CNV;END=104050640;REFLEN=47259\tGT:SM:CN:BC:PE\t1:2.04762:2:35:4,0\n+chrX\t115308311\tDRAGEN:LOSS:chrX:115308312-115309311\tN\t<DEL>\t47\tcnvLength\tSVTYPE=CNV;END=115309311;REFLEN=1000\tGT:SM:CN:BC:PE\t1:1.00369e-09:0:1:15,13\n+chrX\t115735984\tDRAGEN:LOSS:chrX:115735985-115737909\tN\t<DEL>\t53\tcnvLength\tSVTYPE=CNV;END=115737909;REFLEN=1925\tGT:SM:CN:BC:PE\t1:1.00369e-09:0:1:10,10\n+chrX\t119740347\tDRAGEN:LOSS:chrX:119740348-119742168\tN\t<DEL>\t53\tcnvLength\tSVTYPE=CNV;END=119742168;REFLEN=1821\tGT:SM:CN:BC:PE\t1:1.00369e-09:0:1:25,24\n+chrX\t129366304\tDRAGEN:LOSS:chrX:129366305-129368317\tN\t<DEL>\t54\tcnvLength\tSVTYPE=CNV;END=129368317;REFLEN=2013\tGT:SM:CN:BC:PE\t1:1.00369e-09:0:2:26,14\n+chrX\t141382259\tDRAGEN:LOSS:chrX:141382260-141384533\tN\t<DEL>\t55\tcnvLength\tSVTYPE=CNV;END=141384533;REFLEN=2274\tGT:SM:CN:BC:PE\t1:1.00369e-09:0:2:26,26\n+chrX\t143652805\tDRAGEN:LOSS:chrX:143652806-143659126\tN\t<DEL>\t40\tcnvLength\tSVTYPE=CNV;END=143659126;REFLEN=6321\tGT:SM:CN:BC:PE\t1:0.144084:0:2:0,1\n+chrX\t145340613\tDRAGEN:LOSS:chrX:145340614-145342783\tN\t<DEL>\t54\tcnvLength\tSVTYPE=CNV;END=145342783;REFLEN=2170\tGT:SM:CN:BC:PE\t1:1.00369e-09:0:2:8,6\n+chrX\t150759112\tDRAGEN:LOSS:chrX:150759113-150760112\tN\t<DEL>\t45\tcnvLength\tSVTYPE=CNV;END=150760112;REFLEN=1000\tGT:SM:CN:BC:PE\t1:0.0295694:0:1:23,40\n+chrX\t151124830\tDRAGEN:LOSS:chrX:151124831-151127394\tN\t<DEL>\t18\tcnvLength\tSVTYPE=CNV;END=151127394;REFLEN=2564\tGT:SM:CN:BC:PE\t1:0.224926:0:2:14,15\n+chrX\t155688504\tDRAGEN:LOSS:chrX:155688505-155692183\tN\t<DEL>\t60\tcnvLength\tSVTYPE=CNV;END=155692183;REFLEN=3679\tGT:SM:CN:BC:PE\t1:1.00369e-09:0:3:24,30\n+chrY\t3844269\tDRAGEN:GAIN:chrY:3844270-3854396\tN\t<DUP>\t55\tPASS\tSVTYPE=CNV;END=3854396;REFLEN=10127\tGT:SM:CN:BC:PE\t1:1.85714:2:9:12,2\n+chrY\t10659024\tDRAGEN:GAIN:chrY:10659025-10693717\tN\t<DUP>\t79\tPASS\tSVTYPE=CNV;END=10693717;REFLEN=34693\tGT:SM:CN:BC:PE\t1:1.96766:2:14:2544,460\n+chrY\t11108561\tDRAGEN:GAIN:chrY:11108562-11117868\tN\t<DUP>\t116\tcnvLength\tSVTYPE=CNV;END=11117868;REFLEN=9307\tGT:SM:CN:BC:PE\t1:3.54352:4:4:2,22\n+chrY\t11289947\tDRAGEN:GAIN:chrY:11289948-11296309\tN\t<DUP>\t150\tcnvLength\tSVTYPE=CNV;END=11296309;REFLEN=6362\tGT:SM:CN:BC:PE\t1:26.0609:26:5:708,2932\n+chrY\t11296309\tDRAGEN:GAIN:chrY:11296310-11330116\tN\t<DUP>\t67\tPASS\tSVTYPE=CNV;END=11330116;REFLEN=33807\tGT:SM:CN:BC:PE\t1:1.84192:2:23:2932,5446\n+chrY\t11530585\tDRAGEN:GAIN:chrY:11530586-11539539\tN\t<DUP>\t150\tcnvLength\tSVTYPE=CNV;END=11539539;REFLEN=8954\tGT:SM:CN:BC:PE\t1:16.6986:17:6:590,1076\n+chrY\t11744914\tDRAGEN:GAIN:chrY:11744915-11748800\tN\t<DUP>\t57\tcnvLength\tSVTYPE=CNV;END=11748800;REFLEN=3886\tGT:SM:CN:BC:PE\t1:2.03175:2:3:379,1108\n+chrY\t12512335\tDRAGEN:LOSS:chrY:12512336-12514483\tN\t<DEL>\t6\tcnvLength\tSVTYPE=CNV;END=12514483;REFLEN=2148\tGT:SM:CN:BC:PE\t1:0.284822:0:2:3,17\n'
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diff -r 000000000000 -r c8caf812d33b test-data/output.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.json Fri Mar 01 07:19:35 2024 +0000
[
b'@@ -0,0 +1,8867 @@\n+[\n+    {\n+        "biosampleId": "HG00096",\n+        "assemblyId": "GRCh38",\n+        "variantInternalId": "chr1:2650427-2651463:EFO:0030069",\n+        "variantType": "DEL",\n+        "variantId": "EFO:0030069",\n+        "start": 2650427,\n+        "end": 2651463,\n+        "referenceName": "1",\n+        "info": {\n+            "legacyId": "DRAGEN:LOSS:chr1:2650428-2651463",\n+            "cnCount": 0,\n+            "cnValue": 1.00369e-09\n+        }\n+    },\n+    {\n+        "biosampleId": "HG00096",\n+        "assemblyId": "GRCh38",\n+        "variantInternalId": "chr1:2651463-2653075:EFO:0030068",\n+        "variantType": "DEL",\n+        "variantId": "EFO:0030068",\n+        "start": 2651463,\n+        "end": 2653075,\n+        "referenceName": "1",\n+        "info": {\n+            "legacyId": "DRAGEN:LOSS:chr1:2651464-2653075",\n+            "cnCount": 1,\n+            "cnValue": 0.395524\n+        }\n+    },\n+    {\n+        "biosampleId": "HG00096",\n+        "assemblyId": "GRCh38",\n+        "variantInternalId": "chr1:4063594-4067475:EFO:0030068",\n+        "variantType": "DEL",\n+        "variantId": "EFO:0030068",\n+        "start": 4063594,\n+        "end": 4067475,\n+        "referenceName": "1",\n+        "info": {\n+            "legacyId": "DRAGEN:LOSS:chr1:4063595-4067475",\n+            "cnCount": 1,\n+            "cnValue": 0.429788\n+        }\n+    },\n+    {\n+        "biosampleId": "HG00096",\n+        "assemblyId": "GRCh38",\n+        "variantInternalId": "chr1:6377770-6385660:EFO:0030068",\n+        "variantType": "DEL",\n+        "variantId": "EFO:0030068",\n+        "start": 6377770,\n+        "end": 6385660,\n+        "referenceName": "1",\n+        "info": {\n+            "legacyId": "DRAGEN:LOSS:chr1:6377771-6385660",\n+            "cnCount": 1,\n+            "cnValue": 0.543097\n+        }\n+    },\n+    {\n+        "biosampleId": "HG00096",\n+        "assemblyId": "GRCh38",\n+        "variantInternalId": "chr1:8143311-8150440:EFO:0030071",\n+        "variantType": "DUP",\n+        "variantId": "EFO:0030071",\n+        "start": 8143311,\n+        "end": 8150440,\n+        "referenceName": "1",\n+        "info": {\n+            "legacyId": "DRAGEN:GAIN:chr1:8143312-8150440",\n+            "cnCount": 3,\n+            "cnValue": 1.42495\n+        }\n+    },\n+    {\n+        "biosampleId": "HG00096",\n+        "assemblyId": "GRCh38",\n+        "variantInternalId": "chr1:13224579-13242034:EFO:0030071",\n+        "variantType": "DUP",\n+        "variantId": "EFO:0030071",\n+        "start": 13224579,\n+        "end": 13242034,\n+        "referenceName": "1",\n+        "info": {\n+            "legacyId": "DRAGEN:GAIN:chr1:13224580-13242034",\n+            "cnCount": 3,\n+            "cnValue": 1.49181\n+        }\n+    },\n+    {\n+        "biosampleId": "HG00096",\n+        "assemblyId": "GRCh38",\n+        "variantInternalId": "chr1:16605061-16646293:EFO:0030071",\n+        "variantType": "DUP",\n+        "variantId": "EFO:0030071",\n+        "start": 16605061,\n+        "end": 16646293,\n+        "referenceName": "1",\n+        "info": {\n+            "legacyId": "DRAGEN:GAIN:chr1:16605062-16646293",\n+            "cnCount": 7,\n+            "cnValue": 3.3289\n+        }\n+    },\n+    {\n+        "biosampleId": "HG00096",\n+        "assemblyId": "GRCh38",\n+        "variantInternalId": "chr1:16716711-16728256:EFO:0030071",\n+        "variantType": "DUP",\n+        "variantId": "EFO:0030071",\n+        "start": 16716711,\n+        "end": 16728256,\n+        "referenceName": "1",\n+        "info": {\n+            "legacyId": "DRAGEN:GAIN:chr1:16716712-16728256",\n+            "cnCount": 5,\n+            "cnValue": 2.68822\n+        }\n+    },\n+    {\n+        "biosampleId": "HG00096",\n+        "assemblyId": "GRCh38",\n+        "variantInternalId": "chr1:16879751-16950196:EFO:0030071",\n+        "variantType": "DUP",\n+        "variantId": "EFO:0030071",\n+        "start": 16879751,\n+        "end": 16950196,\n+        "referenceName": "1",\n+        "info": {\n+            "legacyId": "DRAGEN:GAIN:'..b'",\n+        "variantType": "DEL",\n+        "variantId": "EFO:0030069",\n+        "start": 155688504,\n+        "end": 155692183,\n+        "referenceName": "X",\n+        "info": {\n+            "legacyId": "DRAGEN:LOSS:chrX:155688505-155692183",\n+            "cnCount": 0,\n+            "cnValue": 1.00369e-09\n+        }\n+    },\n+    {\n+        "biosampleId": "HG00096",\n+        "assemblyId": "GRCh38",\n+        "variantInternalId": "chrY:3844269-3854396:EFO:0030070",\n+        "variantType": "DUP",\n+        "variantId": "EFO:0030070",\n+        "start": 3844269,\n+        "end": 3854396,\n+        "referenceName": "Y",\n+        "info": {\n+            "legacyId": "DRAGEN:GAIN:chrY:3844270-3854396",\n+            "cnCount": 2,\n+            "cnValue": 1.85714\n+        }\n+    },\n+    {\n+        "biosampleId": "HG00096",\n+        "assemblyId": "GRCh38",\n+        "variantInternalId": "chrY:10659024-10693717:EFO:0030070",\n+        "variantType": "DUP",\n+        "variantId": "EFO:0030070",\n+        "start": 10659024,\n+        "end": 10693717,\n+        "referenceName": "Y",\n+        "info": {\n+            "legacyId": "DRAGEN:GAIN:chrY:10659025-10693717",\n+            "cnCount": 2,\n+            "cnValue": 1.96766\n+        }\n+    },\n+    {\n+        "biosampleId": "HG00096",\n+        "assemblyId": "GRCh38",\n+        "variantInternalId": "chrY:11108561-11117868:EFO:0030070",\n+        "variantType": "DUP",\n+        "variantId": "EFO:0030070",\n+        "start": 11108561,\n+        "end": 11117868,\n+        "referenceName": "Y",\n+        "info": {\n+            "legacyId": "DRAGEN:GAIN:chrY:11108562-11117868",\n+            "cnCount": 4,\n+            "cnValue": 3.54352\n+        }\n+    },\n+    {\n+        "biosampleId": "HG00096",\n+        "assemblyId": "GRCh38",\n+        "variantInternalId": "chrY:11289947-11296309:EFO:0030071",\n+        "variantType": "DUP",\n+        "variantId": "EFO:0030071",\n+        "start": 11289947,\n+        "end": 11296309,\n+        "referenceName": "Y",\n+        "info": {\n+            "legacyId": "DRAGEN:GAIN:chrY:11289948-11296309",\n+            "cnCount": 26,\n+            "cnValue": 26.0609\n+        }\n+    },\n+    {\n+        "biosampleId": "HG00096",\n+        "assemblyId": "GRCh38",\n+        "variantInternalId": "chrY:11296309-11330116:EFO:0030070",\n+        "variantType": "DUP",\n+        "variantId": "EFO:0030070",\n+        "start": 11296309,\n+        "end": 11330116,\n+        "referenceName": "Y",\n+        "info": {\n+            "legacyId": "DRAGEN:GAIN:chrY:11296310-11330116",\n+            "cnCount": 2,\n+            "cnValue": 1.84192\n+        }\n+    },\n+    {\n+        "biosampleId": "HG00096",\n+        "assemblyId": "GRCh38",\n+        "variantInternalId": "chrY:11530585-11539539:EFO:0030071",\n+        "variantType": "DUP",\n+        "variantId": "EFO:0030071",\n+        "start": 11530585,\n+        "end": 11539539,\n+        "referenceName": "Y",\n+        "info": {\n+            "legacyId": "DRAGEN:GAIN:chrY:11530586-11539539",\n+            "cnCount": 17,\n+            "cnValue": 16.6986\n+        }\n+    },\n+    {\n+        "biosampleId": "HG00096",\n+        "assemblyId": "GRCh38",\n+        "variantInternalId": "chrY:11744914-11748800:EFO:0030070",\n+        "variantType": "DUP",\n+        "variantId": "EFO:0030070",\n+        "start": 11744914,\n+        "end": 11748800,\n+        "referenceName": "Y",\n+        "info": {\n+            "legacyId": "DRAGEN:GAIN:chrY:11744915-11748800",\n+            "cnCount": 2,\n+            "cnValue": 2.03175\n+        }\n+    },\n+    {\n+        "biosampleId": "HG00096",\n+        "assemblyId": "GRCh38",\n+        "variantInternalId": "chrY:12512335-12514483:EFO:0030069",\n+        "variantType": "DEL",\n+        "variantId": "EFO:0030069",\n+        "start": 12512335,\n+        "end": 12514483,\n+        "referenceName": "Y",\n+        "info": {\n+            "legacyId": "DRAGEN:LOSS:chrY:12512336-12514483",\n+            "cnCount": 0,\n+            "cnValue": 0.284822\n+        }\n+    }\n+]\n\\ No newline at end of file\n'