# HG changeset patch
# User hepcat72
# Date 1534362054 14400
# Node ID 00cab3d2e98b8e4b202e120e3fe30e6008361312

planemo upload

diff -r 000000000000 -r 00cab3d2e98b svtyper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/svtyper.xml	Wed Aug 15 15:40:54 2018 -0400
@@ -0,0 +1,246 @@
+<tool id="svtyper"
+      name="svtyper"
+      version="0.1.0">
+
+    <description>Compute variant genotypes</description>
+
+    <requirements>
+        <requirement type="package" version="0.6.1">svtyper</requirement>
+        <requirement type="package" version="1.9">samtools</requirement>
+    </requirements>
+
+    <version_command>
+        svtyper -h | grep version | cut -d 'v' -f 3
+    </version_command>
+
+    <command detect_errors="aggressive">
+      <![CDATA[
+          #set refln = "ref.fasta"
+          #if $ref
+              samtools faidx '$ref' &&
+              ln -s -f '$ref' '$refln' &&
+              ln -s -f '${ref}.fai' '${refln}.fai' &&
+          #end if
+
+          #set agnostic_files = []
+          #for $i, $aln in enumerate( $alignment_files ):
+              #if $aln
+                  #if $aln.is_of_type("bam"):
+                      ln -s -f '${aln}' '${i}.bam' &&
+                      ln -s -f '${aln.metadata.bam_index}' '${i}.bam.bai' &&
+                      $agnostic_files.append(str($i) + ".bam")
+                  #else:
+                      ln -s -f '${aln}' '${i}.cram' &&
+                      ln -s -f '${aln.metadata.cram_index}' '${i}.cram.crai' &&
+                      $agnostic_files.append(str($i) + ".cram")
+                  #end if
+              #end if
+          #end for
+
+          svtyper
+          -i '$vcf'
+          -B ${",".join(map(str, $agnostic_files))}
+          -o '$vcfout'
+
+          #if $ref
+              -T $refln
+          #end if
+
+          #if $libin
+              -l $libin
+          #elif $outputlib
+              -l $libout
+          #end if
+
+          -m '$minaln'
+          -n '$samplesize'
+
+          #if int($maxreads) > 0
+              --max_reads '$maxreads'
+          #end if
+
+          --split_weight '$splitweight'
+          --disc_weight '$discweight'
+
+          #if $outputbam
+              -w '$bamout'
+          #end if
+
+          > '$vcfout'
+      ]]>
+    </command>
+
+    <inputs>
+        <param name="vcf"
+               label="vcf file"
+               argument="--input_vcf"
+
+               type="data"
+               format="vcf"
+
+               help="VCF input (default: stdin)"/>
+
+        <param name="alignment_files"
+               label="bam/cram file"
+               argument="--bam"
+
+               type="data"
+               format="bam,cram"
+               multiple="true"
+
+               help="BAM or CRAM file(s), comma-separated if genotyping multiple samples" />
+
+        <param name="ref"
+               label="Reference"
+               argument="--ref_fasta"
+
+               type="data"
+               format="fasta"
+               optional="true"
+
+               help="Indexed reference FASTA file (recommended for reading CRAM files)" />
+
+        <param name="libin"
+               label="Library json file"
+               argument="--lib_info"
+
+               type="data"
+               format="json"
+
+               help="read JSON file of library information" />
+
+        <param name="minaln"
+               label="Min aligned bases"
+               argument="--min_aligned"
+
+               type="integer"
+               value="20"
+
+               help="minimum number of aligned bases to consider read as evidence [20]" />
+
+        <param name="samplesize"
+               label="Sampling size for insert size determination"
+               argument="-n"
+
+               type="integer"
+               value="1000000"
+
+               help="number of reads to sample from BAM file for building insert size distribution [1000000]" />
+
+        <param name="sumquals"
+               label="Add genotyping quality"
+               argument="--sum_quals"
+
+               type="boolean"
+               truevalue="-q"
+               falsevalue=""
+               checked="no"
+               value="false"
+
+               help="add genotyping quality to existing QUAL (default: overwrite QUAL field)" />
+
+        <param name="maxreads"
+               label="Max reads to consider per variant"
+               argument="--max_reads"
+
+               type="integer"
+               value="0"
+
+               help="maximum number of reads to assess at any variant (reduces processing time in high-depth regions, default: 0 = unlimited)" />
+
+        <param name="splitweight"
+               label="Split read weight"
+               argument="--split_weight"
+
+               type="float"
+               value="1"
+
+               help="weight for split reads [1]" />
+
+        <param name="discweight"
+               label="Discordant read weight"
+               argument="--disc_weight"
+
+               type="float"
+               value="1"
+
+               help="weight for discordant paired-end reads [1]" />
+
+        <param name="outputlib"
+               label="Create an output library json file"
+
+               type="boolean"
+               checked="no"
+
+               help="if an input library json file (--lib_info) is not provided, create an output library json file" />
+
+        <param name="outputbam"
+               label="Create an output bam file"
+
+               type="boolean"
+               checked="no"
+
+               help="generate an output bam file containing the reads supporting the structural variants" />
+    </inputs>
+
+    <outputs>
+        <data format="vcf" name="vcfout" />
+        <data format="json" name="libout">
+            <filter>outputlib</filter>
+        </data>
+        <data format="bam" name="bamout">
+            <filter>outputbam</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="vcf" value="test1.vcf"/>
+            <param name="alignment_files" value="test1.bam"/>
+            <param name="libin" value="test1.bam.json"/>
+            <output name="vcfout" file="test1.out.vcf"
+                    compare="diff" lines_diff="2" />
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+
+            usage: svtyper [-h] [-i FILE] [-o FILE] -B FILE [-T FILE] [-l FILE] [-m INT]
+                           [-n INT] [-q] [--max_reads INT] [--split_weight FLOAT]
+                           [--disc_weight FLOAT] [-w FILE] [--verbose]
+
+            svtyper
+            author: Colby Chiang (colbychiang@wustl.edu)
+            version: v0.6.0
+            description: Compute genotype of structural variants based on breakpoint depth
+
+            optional arguments:
+              -h, --help            show this help message and exit
+              -i FILE, --input_vcf FILE
+                                    VCF input (default: stdin)
+              -o FILE, --output_vcf FILE
+                                    output VCF to write (default: stdout)
+              -B FILE, --bam FILE   BAM or CRAM file(s), comma-separated if genotyping multiple samples
+              -T FILE, --ref_fasta FILE
+                                    Indexed reference FASTA file (recommended for reading CRAM files)
+              -l FILE, --lib_info FILE
+                                    create/read JSON file of library information
+              -m INT, --min_aligned INT
+                                    minimum number of aligned bases to consider read as evidence [20]
+              -n INT                number of reads to sample from BAM file for building insert size distribution [1000000]
+              -q, --sum_quals       add genotyping quality to existing QUAL (default: overwrite QUAL field)
+              --max_reads INT       maximum number of reads to assess at any variant (reduces processing time in high-depth regions, default: unlimited)
+              --split_weight FLOAT  weight for split reads [1]
+              --disc_weight FLOAT   weight for discordant paired-end reads [1]
+              -w FILE, --write_alignment FILE
+                                    write relevant reads to BAM file
+              --verbose             Report status updates
+
+        ]]>
+    </help>
+
+    <citations>
+        <citation type="doi">10.1038/nmeth.3505</citation>
+    </citations>
+
+  </tool>
diff -r 000000000000 -r 00cab3d2e98b test-data/out.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.vcf	Wed Aug 15 15:40:54 2018 -0400
@@ -0,0 +1,354 @@
+##fileformat=VCFv4.1
+##fileDate=20180815
+##reference=/shared/genomes/b37/full/human_g1k_v37.fasta
+##INFO=<ID=TOOL,Number=1,Type=String,Description="Tool used to generate variant call">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=STR,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format">
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
+##INFO=<ID=BKPTID,Number=.,Type=String,Description="ID of the assembled alternate allele in the assembly file">
+##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend">
+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
+##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
+##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic mutation">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##INFO=<ID=SUP,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">
+##INFO=<ID=PESUP,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">
+##INFO=<ID=SRSUP,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
+##INFO=<ID=EVTYPE,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
+##INFO=<ID=PRIN,Number=0,Type=Flag,Description="Indicates variant as the principal variant in a BEDPE pair">
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=DUP,Description="Duplication">
+##ALT=<ID=INV,Description="Inversion">
+##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">
+##ALT=<ID=INS,Description="Insertion of novel sequence">
+##ALT=<ID=CNV,Description="Copy number variable region">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=SUP,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">
+##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
+##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
+##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
+##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
+##FORMAT=<ID=CNL,Number=.,Type=Float,Description="Copy number genotype likelihood form imprecise events">
+##FORMAT=<ID=NQ,Number=1,Type=Integer,Description="Phred style probability score that the variant is novel">
+##FORMAT=<ID=HAP,Number=1,Type=Integer,Description="Unique haplotype identifier">
+##FORMAT=<ID=AHAP,Number=1,Type=Integer,Description="Unique identifier of ancestral haplotype">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
+##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations">
+##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)">
+##contig=<ID=1,length=249250621>
+##contig=<ID=2,length=243199373>
+##contig=<ID=3,length=198022430>
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+##contig=<ID=X,length=155270560>
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+##contig=<ID=GL000249.1,length=38502>
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+##contig=<ID=GL000238.1,length=39939>
+##contig=<ID=GL000202.1,length=40103>
+##contig=<ID=GL000234.1,length=40531>
+##contig=<ID=GL000232.1,length=40652>
+##contig=<ID=GL000206.1,length=41001>
+##contig=<ID=GL000240.1,length=41933>
+##contig=<ID=GL000236.1,length=41934>
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+##contig=<ID=GL000233.1,length=45941>
+##contig=<ID=GL000204.1,length=81310>
+##contig=<ID=GL000198.1,length=90085>
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+##contig=<ID=GL000192.1,length=547496>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
+2	2798774	72354	C	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-467;END=2799241;STR=+-:840;CIPOS=0,0;CIEND=0,0;EVENT=72354;SUP=840;PESUP=608;SRSUP=232;EVTYPE=PE,SR;PRIN	GT	./.
+2	3732805	72623	C	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-5222;END=3738027;STR=+-:212;CIPOS=0,0;CIEND=0,0;EVENT=72623;SUP=212;PESUP=192;SRSUP=20;EVTYPE=PE,SR;PRIN	GT	./.
+2	6400508	73459	C	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1684;END=6402192;STR=+-:38;CIPOS=0,0;CIEND=0,0;EVENT=73459;SUP=38;PESUP=27;SRSUP=11;EVTYPE=PE,SR;PRIN	GT	./.
+2	14704171	76210	G	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-5944;END=14710115;STR=+-:293;CIPOS=0,0;CIEND=0,0;EVENT=76210;SUP=293;PESUP=218;SRSUP=75;EVTYPE=PE,SR;PRIN	GT	./.
+2	16271643	76851	G	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-2219;END=16273862;STR=+-:196;IMPRECISE;CIPOS=-1,6;CIEND=-5,1;EVENT=76851;SUP=196;PESUP=196;SRSUP=0;EVTYPE=PE;PRIN	GT	./.
+2	18906149	76667	T	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1198;END=18907347;STR=+-:313;CIPOS=0,0;CIEND=0,0;EVENT=76667;SUP=313;PESUP=226;SRSUP=87;EVTYPE=PE,SR;PRIN	GT	./.
+2	28661666	80866	C	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-51;END=28661717;STR=+-:202;CIPOS=0,0;CIEND=0,0;EVENT=80866;SUP=202;PESUP=0;SRSUP=202;EVTYPE=SR;PRIN	GT	./.
+2	30934974	81625	C	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-120;END=30935094;STR=+-:8;CIPOS=0,0;CIEND=0,0;EVENT=81625;SUP=8;PESUP=1;SRSUP=7;EVTYPE=PE,SR;PRIN	GT	./.
+2	33224462	82677	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-2829;END=33227291;STR=+-:357;CIPOS=0,0;CIEND=0,0;EVENT=82677;SUP=357;PESUP=263;SRSUP=94;EVTYPE=PE,SR;PRIN	GT	./.
+2	34523656	83127	G	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-2062;END=34525718;STR=+-:1031;CIPOS=0,0;CIEND=0,0;EVENT=83127;SUP=1031;PESUP=719;SRSUP=312;EVTYPE=PE,SR;PRIN	GT	./.
+2	34965729	83280	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1539;END=34967268;STR=+-:86;CIPOS=0,0;CIEND=0,0;EVENT=83280;SUP=86;PESUP=61;SRSUP=25;EVTYPE=PE,SR;PRIN	GT	./.
+2	35007246	83301	G	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-578;END=35007824;STR=+-:16;CIPOS=0,0;CIEND=0,0;EVENT=83301;SUP=16;PESUP=0;SRSUP=16;EVTYPE=SR;PRIN	GT	./.
+2	35772266	83555	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-52;END=35772318;STR=+-:109;CIPOS=0,0;CIEND=0,0;EVENT=83555;SUP=109;PESUP=1;SRSUP=108;EVTYPE=PE,SR;PRIN	GT	./.
+2	40446947	85115	T	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-125;END=40447072;STR=+-:100;CIPOS=0,0;CIEND=0,0;EVENT=85115;SUP=100;PESUP=0;SRSUP=100;EVTYPE=SR;PRIN	GT	./.
+2	41238369	85376	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-11934;END=41250303;STR=+-:41;CIPOS=0,0;CIEND=0,0;EVENT=85376;SUP=41;PESUP=29;SRSUP=12;EVTYPE=PE,SR;PRIN	GT	./.
+2	41775966	85577	T	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-5316;END=41781282;STR=+-:287;CIPOS=0,0;CIEND=0,0;EVENT=85577;SUP=287;PESUP=227;SRSUP=60;EVTYPE=PE,SR;PRIN	GT	./.
+2	42346259	85762	C	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1086;END=42347345;STR=+-:204;IMPRECISE;CIPOS=-1,13;CIEND=0,0;EVENT=85762;SUP=204;PESUP=204;SRSUP=0;EVTYPE=PE;PRIN	GT	./.
+2	43854262	86202	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-217;END=43854479;STR=+-:57;CIPOS=0,0;CIEND=0,0;EVENT=86202;SUP=57;PESUP=3;SRSUP=54;EVTYPE=PE,SR;PRIN	GT	./.
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diff -r 000000000000 -r 00cab3d2e98b test-data/test1.bam
Binary file test-data/test1.bam has changed
diff -r 000000000000 -r 00cab3d2e98b test-data/test1.bam.bai
Binary file test-data/test1.bam.bai has changed
diff -r 000000000000 -r 00cab3d2e98b test-data/test1.bam.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.bam.json	Wed Aug 15 15:40:54 2018 -0400
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+                }, 
+                "mean": 320.0287878620012, 
+                "sd": 80.21936446609676
+            }
+        ], 
+        "sample_name": "NA12878"
+    }
+}
\ No newline at end of file
diff -r 000000000000 -r 00cab3d2e98b test-data/test1.out.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.out.vcf	Wed Aug 15 15:40:54 2018 -0400
@@ -0,0 +1,354 @@
+##fileformat=VCFv4.1
+##fileDate=20180119
+##reference=/shared/genomes/b37/full/human_g1k_v37.fasta
+##INFO=<ID=TOOL,Number=1,Type=String,Description="Tool used to generate variant call">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=STR,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format">
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
+##INFO=<ID=BKPTID,Number=.,Type=String,Description="ID of the assembled alternate allele in the assembly file">
+##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend">
+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
+##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
+##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic mutation">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##INFO=<ID=SUP,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">
+##INFO=<ID=PESUP,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">
+##INFO=<ID=SRSUP,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
+##INFO=<ID=EVTYPE,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
+##INFO=<ID=PRIN,Number=0,Type=Flag,Description="Indicates variant as the principal variant in a BEDPE pair">
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=DUP,Description="Duplication">
+##ALT=<ID=INV,Description="Inversion">
+##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">
+##ALT=<ID=INS,Description="Insertion of novel sequence">
+##ALT=<ID=CNV,Description="Copy number variable region">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=SUP,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">
+##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
+##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
+##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
+##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
+##FORMAT=<ID=CNL,Number=.,Type=Float,Description="Copy number genotype likelihood form imprecise events">
+##FORMAT=<ID=NQ,Number=1,Type=Integer,Description="Phred style probability score that the variant is novel">
+##FORMAT=<ID=HAP,Number=1,Type=Integer,Description="Unique haplotype identifier">
+##FORMAT=<ID=AHAP,Number=1,Type=Integer,Description="Unique identifier of ancestral haplotype">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
+##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations">
+##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)">
+##contig=<ID=1,length=249250621>
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+##contig=<ID=GL000192.1,length=547496>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
+2	2798774	72354	C	<DEL>	1743.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-467;END=2799241;STR=+-:840;CIPOS=0,0;CIEND=0,0;EVENT=72354;SUP=840;PESUP=608;SRSUP=232;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	1/1:150:60:0:60:1743.00:-177,-18,-3:0:59:0:15:4:0:39:1
+2	3732805	72623	C	<DEL>	755.39	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-5222;END=3738027;STR=+-:212;CIPOS=0,0;CIEND=0,0;EVENT=72623;SUP=212;PESUP=192;SRSUP=20;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:81:46:34:755.39:-77,-1,-24:45:33:21:2:4:24:26:0.42
+2	6400508	73459	C	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1684;END=6402192;STR=+-:38;CIPOS=0,0;CIEND=0,0;EVENT=73459;SUP=38;PESUP=27;SRSUP=11;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:127:127:0:0.00:-0,-38,-126:126:0:65:0:0:61:0:0
+2	14704171	76210	G	<DEL>	1013.14	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-5944;END=14710115;STR=+-:293;CIPOS=0,0;CIEND=0,0;EVENT=76210;SUP=293;PESUP=218;SRSUP=75;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:115:68:46:1013.14:-103,-2,-37:67:45:31:11:2:36:31:0.4
+2	16271643	76851	G	<DEL>	221.88	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-2219;END=16273862;STR=+-:196;IMPRECISE;CIPOS=-1,6;CIEND=-5,1;EVENT=76851;SUP=196;PESUP=196;SRSUP=0;EVTYPE=PE;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:25:16:7:9:221.88:-23,-1,-3:7:9:0:0:0:7:9:0.56
+2	18906149	76667	T	<DEL>	884.01	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1198;END=18907347;STR=+-:313;CIPOS=0,0;CIEND=0,0;EVENT=76667;SUP=313;PESUP=226;SRSUP=87;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:138:93:44:884.01:-93,-5,-58:92:43:39:13:1:53:28:0.32
+2	28661666	80866	C	<DEL>	224.74	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-51;END=28661717;STR=+-:202;CIPOS=0,0;CIEND=0,0;EVENT=80866;SUP=202;PESUP=0;SRSUP=202;EVTYPE=SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:139:36:24:11:224.74:-24,-2,-16:24:11:24:11:0:0:0:0.31
+2	30934974	81625	C	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-120;END=30935094;STR=+-:8;CIPOS=0,0;CIEND=0,0;EVENT=81625;SUP=8;PESUP=1;SRSUP=7;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:186:62:62:0:0.00:-0,-19,-62:62:0:62:0:0:0:0:0
+2	33224462	82677	A	<DEL>	749.25	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-2829;END=33227291;STR=+-:357;CIPOS=0,0;CIEND=0,0;EVENT=82677;SUP=357;PESUP=263;SRSUP=94;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:102:66:36:749.25:-78,-3,-40:65:35:33:11:2:32:21:0.35
+2	34523656	83127	G	<DEL>	1277.09	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-2062;END=34525718;STR=+-:1031;CIPOS=0,0;CIEND=0,0;EVENT=83127;SUP=1031;PESUP=719;SRSUP=312;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:117:61:55:1277.09:-129,-1,-29:60:54:28:17:2:32:34:0.47
+2	34965729	83280	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1539;END=34967268;STR=+-:86;CIPOS=0,0;CIEND=0,0;EVENT=83280;SUP=86;PESUP=61;SRSUP=25;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:127:127:0:0.00:-0,-38,-126:126:0:61:0:0:65:0:0
+2	35007246	83301	G	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-578;END=35007824;STR=+-:16;CIPOS=0,0;CIEND=0,0;EVENT=83301;SUP=16;PESUP=0;SRSUP=16;EVTYPE=SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:147:147:0:0.00:-0,-44,-146:146:0:69:0:0:77:0:0
+2	35772266	83555	A	<DEL>	305.71	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-52;END=35772318;STR=+-:109;CIPOS=0,0;CIEND=0,0;EVENT=83555;SUP=109;PESUP=1;SRSUP=108;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:132:39:24:14:305.71:-32,-1,-15:24:14:24:14:0:0:0:0.37
+2	40446947	85115	T	<DEL>	155.73	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-125;END=40447072;STR=+-:100;CIPOS=0,0;CIEND=0,0;EVENT=85115;SUP=100;PESUP=0;SRSUP=100;EVTYPE=SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:155:39:29:9:155.73:-19,-3,-21:29:9:29:9:0:0:0:0.24
+2	41238369	85376	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-11934;END=41250303;STR=+-:41;CIPOS=0,0;CIEND=0,0;EVENT=85376;SUP=41;PESUP=29;SRSUP=12;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:135:135:0:0.00:-0,-40,-134:134:0:60:0:0:74:0:0
+2	41775966	85577	T	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-5316;END=41781282;STR=+-:287;CIPOS=0,0;CIEND=0,0;EVENT=85577;SUP=287;PESUP=227;SRSUP=60;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:158:158:0:0.00:-0,-47,-157:157:0:80:0:0:77:0:0
+2	42346259	85762	C	<DEL>	512.36	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1086;END=42347345;STR=+-:204;IMPRECISE;CIPOS=-1,13;CIEND=0,0;EVENT=85762;SUP=204;PESUP=204;SRSUP=0;EVTYPE=PE;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:92:64:27:512.36:-56,-4,-42:63:26:31:3:2:32:21:0.29
+2	43854262	86202	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-217;END=43854479;STR=+-:57;CIPOS=0,0;CIEND=0,0;EVENT=86202;SUP=57;PESUP=3;SRSUP=54;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:149:149:0:0.00:-0,-45,-148:148:0:72:0:0:76:0:0
+2	48851192	87923	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-6759;END=48857951;STR=+-:521;CIPOS=0,0;CIEND=0,0;EVENT=87923;SUP=521;PESUP=381;SRSUP=140;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:144:144:0:0.00:-0,-43,-143:143:0:70:0:0:73:0:0
+2	48990526	87970	T	<DEL>	563.33	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-637;END=48991163;STR=+-:458;CIPOS=0,0;CIEND=0,0;EVENT=87970;SUP=458;PESUP=314;SRSUP=144;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:95:65:29:563.33:-61,-4,-42:64:28:30:6:3:34:18:0.3
+2	49561484	88177	G	<DEL>	620.39	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-141;END=49561625;STR=+-:163;CIPOS=0,0;CIEND=0,0;EVENT=88177;SUP=163;PESUP=3;SRSUP=160;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	1/1:53:21:0:21:620.39:-63,-6,-1:0:21:0:21:0:0:0:1
+2	51926587	88990	A	<DEL>	722.26	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1179;END=51927766;STR=+-:383;CIPOS=0,0;CIEND=0,0;EVENT=88990;SUP=383;PESUP=273;SRSUP=110;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:102:66:35:722.26:-75,-3,-40:65:34:25:7:3:40:23:0.34
+2	51973823	89011	A	<DEL>	1130.11	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-416;END=51974239;STR=+-:76;CIPOS=0,0;CIEND=0,0;EVENT=89011;SUP=76;PESUP=0;SRSUP=76;EVTYPE=SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:115:65:50:1130.11:-115,-2,-34:64:49:31:6:7:33:35:0.43
+2	52749686	89272	A	<DEL>	1920.26	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-35583;END=52785269;STR=+-:464;CIPOS=0,0;CIEND=0,0;EVENT=89272;SUP=464;PESUP=363;SRSUP=101;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	1/1:165:66:0:66:1920.26:-195,-20,-3:0:65:0:14:7:0:43:1
+2	53166721	89415	G	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-15492;END=53182213;STR=+-:375;CIPOS=0,0;CIEND=0,0;EVENT=89415;SUP=375;PESUP=258;SRSUP=117;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:143:143:0:0.00:-0,-43,-142:142:0:71:0:0:71:0:0
+2	54565493	89901	G	<DEL>	2156.60	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1979;END=54567472;STR=+-:708;CIPOS=0,0;CIEND=0,0;EVENT=89901;SUP=708;PESUP=604;SRSUP=104;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	1/1:186:74:0:74:2156.60:-219,-22,-3:0:73:0:11:10:0:51:1
+2	56071108	90398	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-288;END=56071396;STR=+-:31;CIPOS=0,0;CIEND=0,0;EVENT=90398;SUP=31;PESUP=1;SRSUP=30;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:112:111:0:0.00:-0,-33,-110:110:0:40:0:0:70:0:0
+2	56652247	82193	G	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-3645;END=56655892;STR=+-:57;IMPRECISE;CIPOS=-2,18;CIEND=0,0;EVENT=82193;SUP=57;PESUP=57;SRSUP=0;EVTYPE=PE;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:129:129:0:0.00:-0,-39,-128:128:0:58:0:0:70:0:0
+2	59623256	91676	T	<DEL>	821.08	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-7791;END=59631047;STR=+-:225;CIPOS=0,0;CIEND=0,0;EVENT=91676;SUP=225;PESUP=180;SRSUP=45;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:129:87:41:821.08:-87,-5,-55:86:40:41:10:2:45:27:0.32
+2	61880174	92462	C	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-931;END=61881105;STR=+-:110;CIPOS=0,0;CIEND=0,0;EVENT=92462;SUP=110;PESUP=1;SRSUP=109;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:130:130:0:0.00:-0,-39,-129:129:0:60:0:0:69:0:0
+2	62916470	92781	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-5164;END=62921634;STR=+-:32;CIPOS=0,0;CIEND=0,0;EVENT=92781;SUP=32;PESUP=22;SRSUP=10;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:136:136:0:0.00:-0,-41,-135:135:0:60:0:0:75:0:0
+2	64479691	93866	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-4887;END=64484578;STR=+-:15;IMPRECISE;CIPOS=-1,86;CIEND=0,0;EVENT=93866;SUP=15;PESUP=15;SRSUP=0;EVTYPE=PE;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:99:99:0:0.00:-0,-30,-98:98:0:47:0:0:51:0:0
+2	66505594	94494	T	<DEL>	842.31	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1958;END=66507552;STR=+-:235;CIPOS=0,0;CIEND=0,0;EVENT=94494;SUP=235;PESUP=167;SRSUP=68;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:92:53:38:842.31:-86,-2,-29:52:37:24:6:3:28:27:0.42
+2	67974877	94992	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-201;END=67975078;STR=+-:10;CIPOS=0,0;CIEND=0,0;EVENT=94992;SUP=10;PESUP=0;SRSUP=10;EVTYPE=SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:149:148:0:0.00:-0,-44,-147:147:0:71:0:0:76:0:0
+2	70125053	95759	G	<DEL>	2629.28	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-511;END=70125564;STR=+-:626;CIPOS=0,0;CIEND=0,0;EVENT=95759;SUP=626;PESUP=406;SRSUP=220;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	1/1:200:90:0:90:2629.28:-267,-27,-4:0:89:0:28:5:0:55:1
+2	72440497	96464	T	<INV>	0.00	.	TOOL=LUMPY;SVTYPE=INV;SVLEN=875;END=72441372;STR=++:59;CIPOS=0,0;CIEND=0,0;EVENT=96464;SUP=59;PESUP=46;SRSUP=13;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:142:142:0:0.00:-0,-42,-141:141:0:69:0:0:72:0:0
+2	76557057	97814	T	<DEL>	1978.01	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-232;END=76557289;STR=+-:396;CIPOS=0,0;CIEND=0,0;EVENT=97814;SUP=396;PESUP=59;SRSUP=337;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	1/1:115:81:9:71:1978.01:-199,-12,-1:9:70:0:19:8:9:42:0.89
+2	76773553	93354	T	<DEL>	1358.95	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1898;END=76775451;STR=+-:690;CIPOS=0,0;CIEND=0,0;EVENT=93354;SUP=690;PESUP=480;SRSUP=210;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	1/1:117:47:0:47:1358.95:-138,-14,-2:0:46:0:13:3:0:29:1
+2	76844758	97908	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-756;END=76845514;STR=+-:34;CIPOS=0,0;CIEND=0,0;EVENT=97908;SUP=34;PESUP=25;SRSUP=9;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:149:149:0:0.00:-0,-45,-148:148:0:73:0:0:75:0:0
+2	78117891	98320	A	<DEL>	575.35	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-465;END=78118356;STR=+-:78;CIPOS=0,0;CIEND=0,0;EVENT=98320;SUP=78;PESUP=0;SRSUP=78;EVTYPE=SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:90:61:29:575.35:-61,-4,-38:60:28:25:5:3:35:19:0.32
+2	79076572	98633	T	<DEL>	2363.39	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-4633;END=79081205;STR=+-:638;CIPOS=0,0;CIEND=0,0;EVENT=98633;SUP=638;PESUP=473;SRSUP=165;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	1/1:200:81:0:81:2363.39:-240,-24,-4:0:80:0:19:7:0:54:1
+2	82757145	99771	T	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-298;END=82757443;STR=+-:81;CIPOS=0,0;CIEND=0,0;EVENT=99771;SUP=81;PESUP=39;SRSUP=42;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:142:141:0:0.00:-0,-42,-140:140:0:62:0:0:78:0:0
+2	83035648	99868	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-778;END=83036426;STR=+-:23;CIPOS=0,0;CIEND=0,0;EVENT=99868;SUP=23;PESUP=0;SRSUP=23;EVTYPE=SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:135:135:0:0.00:-0,-40,-134:134:0:61:0:0:73:0:0
+2	84918760	100466	C	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-50;END=84918810;STR=+-:9;CIPOS=0,0;CIEND=0,0;EVENT=100466;SUP=9;PESUP=0;SRSUP=9;EVTYPE=SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:198:66:66:0:0.00:-0,-20,-66:66:0:66:0:0:0:0:0
+2	88429841	101169	G	<DEL>	119.41	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-310;END=88430151;STR=+-:223;CIPOS=0,0;CIEND=0,0;EVENT=101169;SUP=223;PESUP=0;SRSUP=223;EVTYPE=SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:119:93:78:14:119.41:-24,-12,-62:77:13:22:9:0:55:3:0.14
+2	97854310	101962	A	<DEL>	341.72	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1823;END=97856133;STR=+-:208;IMPRECISE;CIPOS=-6,6;CIEND=-18,2;EVENT=101962;SUP=208;PESUP=208;SRSUP=0;EVTYPE=PE;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:108:37:21:15:341.72:-35,-1,-12:21:15:0:0:0:21:15:0.42
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+3	149585150	199828	T	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-3748;END=149588898;STR=+-:38;IMPRECISE;CIPOS=-1,24;CIEND=-20,0;EVENT=199828;SUP=38;PESUP=38;SRSUP=0;EVTYPE=PE;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:119:119:0:0.00:-0,-36,-118:118:0:53:0:0:65:0:0
+3	156092170	202083	C	<DEL>	725.20	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1520;END=156093690;STR=+-:208;IMPRECISE;CIPOS=-1,0;CIEND=-1,0;EVENT=202083;SUP=208;PESUP=205;SRSUP=3;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:111:74:36:725.20:-77,-4,-46:73:35:38:6:2:35:26:0.32
+3	158350740	202825	C	<DEL>	881.19	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1170;END=158351910;STR=+-:532;CIPOS=0,0;CIEND=0,0;EVENT=202825;SUP=532;PESUP=404;SRSUP=128;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:109:67:41:881.19:-91,-2,-38:66:40:26:9:3:40:27:0.38
+3	159257021	203116	T	<DEL>	1193.05	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-668;END=159257689;STR=+-:97;CIPOS=0,0;CIEND=0,0;EVENT=203116;SUP=97;PESUP=0;SRSUP=97;EVTYPE=SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:125:71:53:1193.05:-121,-2,-37:70:52:33:10:3:37:38:0.43
+3	159461398	203186	T	<DEL>	815.51	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-2029;END=159463427;STR=+-:205;IMPRECISE;CIPOS=-1,4;CIEND=-4,3;EVENT=203186;SUP=205;PESUP=205;SRSUP=0;EVTYPE=PE;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:90:59:25:33:815.51:-83,-1,-10:25:33:0:0:0:25:33:0.57
+3	162764901	204292	T	<DEL>	2067.97	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-4182;END=162769083;STR=+-:606;CIPOS=0,0;CIEND=0,0;EVENT=204292;SUP=606;PESUP=493;SRSUP=113;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	1/1:178:71:0:71:2067.97:-210,-21,-3:0:70:0:15:3:0:51:1
+3	168738456	206237	T	<DEL>	2570.19	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-378;END=168738834;STR=+-:205;CIPOS=0,0;CIEND=0,0;EVENT=206237;SUP=205;PESUP=0;SRSUP=205;EVTYPE=SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	1/1:200:88:0:88:2570.19:-261,-26,-4:0:87:0:16:7:0:63:1
+3	172173327	207457	G	<INV>	0.00	.	TOOL=LUMPY;SVTYPE=INV;SVLEN=376;END=172173703;STR=--:221;CIPOS=0,0;CIEND=0,0;EVENT=207457;SUP=221;PESUP=161;SRSUP=60;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:127:127:0:0.00:-0,-38,-126:126:0:61:0:0:65:0:0
+3	177294510	209224	A	<DEL>	593.39	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-2962;END=177297472;STR=+-:261;CIPOS=0,0;CIEND=0,0;EVENT=209224;SUP=261;PESUP=177;SRSUP=84;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:85:55:29:593.39:-62,-3,-33:54:28:23:6:1:31:20:0.34
+3	177381310	209247	T	<DEL>	224.62	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-4161;END=177385471;STR=+-:23;IMPRECISE;CIPOS=-2,58;CIEND=0,0;EVENT=209247;SUP=23;PESUP=23;SRSUP=0;EVTYPE=PE;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:55:42:13:224.62:-27,-4,-30:42:13:0:0:0:42:13:0.24
+3	178550130	209676	G	<DEL>	749.19	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-744;END=178550874;STR=+-:992;CIPOS=0,0;CIEND=0,0;EVENT=209676;SUP=992;PESUP=779;SRSUP=213;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:113:75:37:749.19:-79,-4,-47:74:36:35:4:0:39:31:0.33
+3	178567653	209686	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-689;END=178568342;STR=+-:77;CIPOS=0,0;CIEND=0,0;EVENT=209686;SUP=77;PESUP=2;SRSUP=75;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:160:160:0:0.00:-0,-48,-159:159:0:78:0:0:81:0:0
+3	179654341	210032	C	<DEL>	3131.50	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-462;END=179654803;STR=+-:1342;CIPOS=0,0;CIEND=0,0;EVENT=210032;SUP=1342;PESUP=956;SRSUP=386;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	1/1:200:107:0:107:3131.50:-318,-32,-5:0:106:0:30:6:0:69:1
+3	185628683	211946	G	<DUP>	0.10	.	TOOL=LUMPY;SVTYPE=DUP;SVLEN=80531;END=185709214;STR=-+:103;IMPRECISE;CIPOS=-41,1;CIEND=-2,8;EVENT=211946;SUP=103;PESUP=103;SRSUP=0;EVTYPE=PE;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:16:64:60:3:0.10:-2,-3,-7:60:3:0:0:0:60:3:0.048
+3	187732908	212594	A	<DEL>	224.62	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1909;END=187734817;STR=+-:118;IMPRECISE;CIPOS=-2,8;CIEND=-10,1;EVENT=212594;SUP=118;PESUP=118;SRSUP=0;EVTYPE=PE;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:56:42:13:224.62:-27,-4,-30:42:13:0:0:0:42:13:0.24
+3	189224507	213103	C	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-874;END=189225381;STR=+-:9;CIPOS=0,0;CIEND=0,0;EVENT=213103;SUP=9;PESUP=1;SRSUP=8;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:161:161:0:0.00:-0,-48,-160:160:0:76:0:0:84:0:0
+3	189363422	213158	T	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-7487;END=189370909;STR=+-:132;IMPRECISE;CIPOS=-1,11;CIEND=0,0;EVENT=213158;SUP=132;PESUP=132;SRSUP=0;EVTYPE=PE;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:129:129:0:0.00:-0,-39,-128:128:0:58:0:0:70:0:0
+3	190478458	213572	T	<DEL>	1493.31	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-175;END=190478633;STR=+-:151;CIPOS=0,0;CIEND=0,0;EVENT=213572;SUP=151;PESUP=10;SRSUP=141;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:19:84:24:59:1493.31:-153,-4,-6:24:58:0:16:9:24:32:0.71
+3	192673320	214366	T	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-66;END=192673386;STR=+-:108;CIPOS=0,0;CIEND=0,0;EVENT=214366;SUP=108;PESUP=1;SRSUP=107;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:70:70:0:0.00:-0,-21,-70:70:0:70:0:0:0:0:0
+3	192744355	214380	T	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-537;END=192744892;STR=+-:229;CIPOS=0,0;CIEND=0,0;EVENT=214380;SUP=229;PESUP=217;SRSUP=12;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:121:121:0:0.00:-0,-36,-120:120:0:55:0:0:65:0:0
+3	192875332	214421	T	<DEL>	824.15	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-10072;END=192885404;STR=+-:734;CIPOS=0,0;CIEND=0,0;EVENT=214421;SUP=734;PESUP=499;SRSUP=235;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:118:77:40:824.15:-86,-4,-47:76:39:39:12:2:37:24:0.34
+3	194398752	214899	C	<DEL>	954.46	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1548;END=194400300;STR=+-:293;IMPRECISE;CIPOS=-1,2;CIEND=0,0;EVENT=214899;SUP=293;PESUP=293;SRSUP=0;EVTYPE=PE;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	1/1:51:40:5:34:954.46:-96,-6,-1:5:34:0:0:0:5:34:0.87
+3	195457294	215225	G	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-13713;END=195471007;STR=+-:71;IMPRECISE;CIPOS=-2,9;CIEND=0,0;EVENT=215225;SUP=71;PESUP=71;SRSUP=0;EVTYPE=PE;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:127:127:0:0.00:-0,-38,-126:126:0:61:0:0:65:0:0
+3	195569217	215275	G	<DEL>	647.37	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-724;END=195569941;STR=+-:385;CIPOS=0,0;CIEND=0,0;EVENT=215275;SUP=385;PESUP=362;SRSUP=23;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:87:55:31:647.37:-67,-3,-33:54:30:23:0:2:31:27:0.36
+3	195949296	215374	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-2004;END=195951300;STR=+-:229;IMPRECISE;CIPOS=-1,3;CIEND=0,0;EVENT=215374;SUP=229;PESUP=229;SRSUP=0;EVTYPE=PE;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:129:129:0:0.00:-0,-39,-128:128:0:53:0:0:75:0:0
+3	196934573	215670	A	<DEL>	920.21	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-4681;END=196939254;STR=+-:349;CIPOS=0,0;CIEND=0,0;EVENT=215670;SUP=349;PESUP=259;SRSUP=90;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:106:63:42:920.21:-94,-2,-35:62:41:27:9:3:35:28:0.4
+2	84728755	894054_1	A	A]15:89212842]	65.75	.	TOOL=LUMPY;SVTYPE=BND;STR=++:74;IMPRECISE;CIPOS=-1,2;CIEND=0,0;MATEID=894054_2;EVENT=894054;SUP=74;PESUP=73;SRSUP=1;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:65:39:32:6:65.75:-12,-5,-26:32:6:0:0:0:32:6:0.16
+15	89212842	894054_2	C	C]2:84728755]	65.75	.	TOOL=LUMPY;SVTYPE=BND;STR=++:74;IMPRECISE;CIPOS=0,0;CIEND=-1,2;MATEID=894054_1;EVENT=894054;SUP=74;PESUP=73;SRSUP=1;EVTYPE=PE,SR	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:65:39:32:6:65.75:-12,-5,-26:32:6:0:0:0:32:6:0.16
diff -r 000000000000 -r 00cab3d2e98b test-data/test1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.vcf	Wed Aug 15 15:40:54 2018 -0400
@@ -0,0 +1,344 @@
+##fileformat=VCFv4.1
+##fileDate=20140901
+##reference=/shared/genomes/b37/full/human_g1k_v37.fasta
+##INFO=<ID=TOOL,Number=1,Type=String,Description="Tool used to generate variant call">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=STR,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format">
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
+##INFO=<ID=BKPTID,Number=.,Type=String,Description="ID of the assembled alternate allele in the assembly file">
+##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend">
+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
+##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
+##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic mutation">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##INFO=<ID=SUP,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">
+##INFO=<ID=PESUP,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">
+##INFO=<ID=SRSUP,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
+##INFO=<ID=EVTYPE,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
+##INFO=<ID=PRIN,Number=0,Type=Flag,Description="Indicates variant as the principal variant in a BEDPE pair">
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=DUP,Description="Duplication">
+##ALT=<ID=INV,Description="Inversion">
+##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">
+##ALT=<ID=INS,Description="Insertion of novel sequence">
+##ALT=<ID=CNV,Description="Copy number variable region">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=SUP,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">
+##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
+##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
+##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
+##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
+##FORMAT=<ID=CNL,Number=.,Type=Float,Description="Copy number genotype likelihood form imprecise events">
+##FORMAT=<ID=NQ,Number=1,Type=Integer,Description="Phred style probability score that the variant is novel">
+##FORMAT=<ID=HAP,Number=1,Type=Integer,Description="Unique haplotype identifier">
+##FORMAT=<ID=AHAP,Number=1,Type=Integer,Description="Unique identifier of ancestral haplotype">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
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+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+2	2798774	72354	C	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-467;END=2799241;STR=+-:840;CIPOS=0,0;CIEND=0,0;EVENT=72354;SUP=840;PESUP=608;SRSUP=232;EVTYPE=PE,SR;PRIN
+2	3732805	72623	C	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-5222;END=3738027;STR=+-:212;CIPOS=0,0;CIEND=0,0;EVENT=72623;SUP=212;PESUP=192;SRSUP=20;EVTYPE=PE,SR;PRIN
+2	6400508	73459	C	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1684;END=6402192;STR=+-:38;CIPOS=0,0;CIEND=0,0;EVENT=73459;SUP=38;PESUP=27;SRSUP=11;EVTYPE=PE,SR;PRIN
+2	14704171	76210	G	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-5944;END=14710115;STR=+-:293;CIPOS=0,0;CIEND=0,0;EVENT=76210;SUP=293;PESUP=218;SRSUP=75;EVTYPE=PE,SR;PRIN
+2	16271643	76851	G	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-2219;END=16273862;STR=+-:196;IMPRECISE;CIPOS=-1,6;CIEND=-5,1;EVENT=76851;SUP=196;PESUP=196;SRSUP=0;EVTYPE=PE;PRIN
+2	18906149	76667	T	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1198;END=18907347;STR=+-:313;CIPOS=0,0;CIEND=0,0;EVENT=76667;SUP=313;PESUP=226;SRSUP=87;EVTYPE=PE,SR;PRIN
+2	28661666	80866	C	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-51;END=28661717;STR=+-:202;CIPOS=0,0;CIEND=0,0;EVENT=80866;SUP=202;PESUP=0;SRSUP=202;EVTYPE=SR;PRIN
+2	30934974	81625	C	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-120;END=30935094;STR=+-:8;CIPOS=0,0;CIEND=0,0;EVENT=81625;SUP=8;PESUP=1;SRSUP=7;EVTYPE=PE,SR;PRIN
+2	33224462	82677	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-2829;END=33227291;STR=+-:357;CIPOS=0,0;CIEND=0,0;EVENT=82677;SUP=357;PESUP=263;SRSUP=94;EVTYPE=PE,SR;PRIN
+2	34523656	83127	G	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-2062;END=34525718;STR=+-:1031;CIPOS=0,0;CIEND=0,0;EVENT=83127;SUP=1031;PESUP=719;SRSUP=312;EVTYPE=PE,SR;PRIN
+2	34965729	83280	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1539;END=34967268;STR=+-:86;CIPOS=0,0;CIEND=0,0;EVENT=83280;SUP=86;PESUP=61;SRSUP=25;EVTYPE=PE,SR;PRIN
+2	35007246	83301	G	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-578;END=35007824;STR=+-:16;CIPOS=0,0;CIEND=0,0;EVENT=83301;SUP=16;PESUP=0;SRSUP=16;EVTYPE=SR;PRIN
+2	35772266	83555	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-52;END=35772318;STR=+-:109;CIPOS=0,0;CIEND=0,0;EVENT=83555;SUP=109;PESUP=1;SRSUP=108;EVTYPE=PE,SR;PRIN
+2	40446947	85115	T	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-125;END=40447072;STR=+-:100;CIPOS=0,0;CIEND=0,0;EVENT=85115;SUP=100;PESUP=0;SRSUP=100;EVTYPE=SR;PRIN
+2	41238369	85376	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-11934;END=41250303;STR=+-:41;CIPOS=0,0;CIEND=0,0;EVENT=85376;SUP=41;PESUP=29;SRSUP=12;EVTYPE=PE,SR;PRIN
+2	41775966	85577	T	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-5316;END=41781282;STR=+-:287;CIPOS=0,0;CIEND=0,0;EVENT=85577;SUP=287;PESUP=227;SRSUP=60;EVTYPE=PE,SR;PRIN
+2	42346259	85762	C	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1086;END=42347345;STR=+-:204;IMPRECISE;CIPOS=-1,13;CIEND=0,0;EVENT=85762;SUP=204;PESUP=204;SRSUP=0;EVTYPE=PE;PRIN
+2	43854262	86202	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-217;END=43854479;STR=+-:57;CIPOS=0,0;CIEND=0,0;EVENT=86202;SUP=57;PESUP=3;SRSUP=54;EVTYPE=PE,SR;PRIN
+2	48851192	87923	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-6759;END=48857951;STR=+-:521;CIPOS=0,0;CIEND=0,0;EVENT=87923;SUP=521;PESUP=381;SRSUP=140;EVTYPE=PE,SR;PRIN
+2	48990526	87970	T	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-637;END=48991163;STR=+-:458;CIPOS=0,0;CIEND=0,0;EVENT=87970;SUP=458;PESUP=314;SRSUP=144;EVTYPE=PE,SR;PRIN
+2	49561484	88177	G	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-141;END=49561625;STR=+-:163;CIPOS=0,0;CIEND=0,0;EVENT=88177;SUP=163;PESUP=3;SRSUP=160;EVTYPE=PE,SR;PRIN
+2	51926587	88990	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1179;END=51927766;STR=+-:383;CIPOS=0,0;CIEND=0,0;EVENT=88990;SUP=383;PESUP=273;SRSUP=110;EVTYPE=PE,SR;PRIN
+2	51973823	89011	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-416;END=51974239;STR=+-:76;CIPOS=0,0;CIEND=0,0;EVENT=89011;SUP=76;PESUP=0;SRSUP=76;EVTYPE=SR;PRIN
+2	52749686	89272	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-35583;END=52785269;STR=+-:464;CIPOS=0,0;CIEND=0,0;EVENT=89272;SUP=464;PESUP=363;SRSUP=101;EVTYPE=PE,SR;PRIN
+2	53166721	89415	G	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-15492;END=53182213;STR=+-:375;CIPOS=0,0;CIEND=0,0;EVENT=89415;SUP=375;PESUP=258;SRSUP=117;EVTYPE=PE,SR;PRIN
+2	54565493	89901	G	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1979;END=54567472;STR=+-:708;CIPOS=0,0;CIEND=0,0;EVENT=89901;SUP=708;PESUP=604;SRSUP=104;EVTYPE=PE,SR;PRIN
+2	56071108	90398	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-288;END=56071396;STR=+-:31;CIPOS=0,0;CIEND=0,0;EVENT=90398;SUP=31;PESUP=1;SRSUP=30;EVTYPE=PE,SR;PRIN
+2	56652247	82193	G	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-3645;END=56655892;STR=+-:57;IMPRECISE;CIPOS=-2,18;CIEND=0,0;EVENT=82193;SUP=57;PESUP=57;SRSUP=0;EVTYPE=PE;PRIN
+2	59623256	91676	T	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-7791;END=59631047;STR=+-:225;CIPOS=0,0;CIEND=0,0;EVENT=91676;SUP=225;PESUP=180;SRSUP=45;EVTYPE=PE,SR;PRIN
+2	61880174	92462	C	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-931;END=61881105;STR=+-:110;CIPOS=0,0;CIEND=0,0;EVENT=92462;SUP=110;PESUP=1;SRSUP=109;EVTYPE=PE,SR;PRIN
+2	62916470	92781	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-5164;END=62921634;STR=+-:32;CIPOS=0,0;CIEND=0,0;EVENT=92781;SUP=32;PESUP=22;SRSUP=10;EVTYPE=PE,SR;PRIN
+2	64479691	93866	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-4887;END=64484578;STR=+-:15;IMPRECISE;CIPOS=-1,86;CIEND=0,0;EVENT=93866;SUP=15;PESUP=15;SRSUP=0;EVTYPE=PE;PRIN
+2	66505594	94494	T	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1958;END=66507552;STR=+-:235;CIPOS=0,0;CIEND=0,0;EVENT=94494;SUP=235;PESUP=167;SRSUP=68;EVTYPE=PE,SR;PRIN
+2	67974877	94992	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-201;END=67975078;STR=+-:10;CIPOS=0,0;CIEND=0,0;EVENT=94992;SUP=10;PESUP=0;SRSUP=10;EVTYPE=SR;PRIN
+2	70125053	95759	G	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-511;END=70125564;STR=+-:626;CIPOS=0,0;CIEND=0,0;EVENT=95759;SUP=626;PESUP=406;SRSUP=220;EVTYPE=PE,SR;PRIN
+2	72440497	96464	T	<INV>	0	.	TOOL=LUMPY;SVTYPE=INV;SVLEN=875;END=72441372;STR=++:59;CIPOS=0,0;CIEND=0,0;EVENT=96464;SUP=59;PESUP=46;SRSUP=13;EVTYPE=PE,SR;PRIN
+2	76557057	97814	T	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-232;END=76557289;STR=+-:396;CIPOS=0,0;CIEND=0,0;EVENT=97814;SUP=396;PESUP=59;SRSUP=337;EVTYPE=PE,SR;PRIN
+2	76773553	93354	T	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1898;END=76775451;STR=+-:690;CIPOS=0,0;CIEND=0,0;EVENT=93354;SUP=690;PESUP=480;SRSUP=210;EVTYPE=PE,SR;PRIN
+2	76844758	97908	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-756;END=76845514;STR=+-:34;CIPOS=0,0;CIEND=0,0;EVENT=97908;SUP=34;PESUP=25;SRSUP=9;EVTYPE=PE,SR;PRIN
+2	78117891	98320	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-465;END=78118356;STR=+-:78;CIPOS=0,0;CIEND=0,0;EVENT=98320;SUP=78;PESUP=0;SRSUP=78;EVTYPE=SR;PRIN
+2	79076572	98633	T	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-4633;END=79081205;STR=+-:638;CIPOS=0,0;CIEND=0,0;EVENT=98633;SUP=638;PESUP=473;SRSUP=165;EVTYPE=PE,SR;PRIN
+2	82757145	99771	T	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-298;END=82757443;STR=+-:81;CIPOS=0,0;CIEND=0,0;EVENT=99771;SUP=81;PESUP=39;SRSUP=42;EVTYPE=PE,SR;PRIN
+2	83035648	99868	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-778;END=83036426;STR=+-:23;CIPOS=0,0;CIEND=0,0;EVENT=99868;SUP=23;PESUP=0;SRSUP=23;EVTYPE=SR;PRIN
+2	84728755	894054_1	A	A]15:89212842]	0	.	TOOL=LUMPY;SVTYPE=BND;STR=++:74;IMPRECISE;CIPOS=-1,2;CIEND=0,0;MATEID=894054_2;EVENT=894054;SUP=74;PESUP=73;SRSUP=1;EVTYPE=PE,SR;PRIN
+2	84918760	100466	C	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-50;END=84918810;STR=+-:9;CIPOS=0,0;CIEND=0,0;EVENT=100466;SUP=9;PESUP=0;SRSUP=9;EVTYPE=SR;PRIN
+2	88429841	101169	G	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-310;END=88430151;STR=+-:223;CIPOS=0,0;CIEND=0,0;EVENT=101169;SUP=223;PESUP=0;SRSUP=223;EVTYPE=SR;PRIN
+2	97854310	101962	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1823;END=97856133;STR=+-:208;IMPRECISE;CIPOS=-6,6;CIEND=-18,2;EVENT=101962;SUP=208;PESUP=208;SRSUP=0;EVTYPE=PE;PRIN
+2	100103713	102623	G	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1317;END=100105030;STR=+-:427;CIPOS=0,0;CIEND=0,0;EVENT=102623;SUP=427;PESUP=341;SRSUP=86;EVTYPE=PE,SR;PRIN
+2	102232584	103227	C	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1002;END=102233586;STR=+-:238;CIPOS=0,0;CIEND=0,0;EVENT=103227;SUP=238;PESUP=115;SRSUP=123;EVTYPE=PE,SR;PRIN
+2	106695078	104660	T	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-815;END=106695893;STR=+-:450;CIPOS=0,0;CIEND=0,0;EVENT=104660;SUP=450;PESUP=317;SRSUP=133;EVTYPE=PE,SR;PRIN
+2	108275311	105097	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-3796;END=108279107;STR=+-:28;CIPOS=0,0;CIEND=0,0;EVENT=105097;SUP=28;PESUP=23;SRSUP=5;EVTYPE=PE,SR;PRIN
+2	108855418	105260	C	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-862;END=108856280;STR=+-:71;CIPOS=0,0;CIEND=0,0;EVENT=105260;SUP=71;PESUP=1;SRSUP=70;EVTYPE=PE,SR;PRIN
+2	109310553	105403	G	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1566;END=109312119;STR=+-:134;IMPRECISE;CIPOS=-1,5;CIEND=0,0;EVENT=105403;SUP=134;PESUP=134;SRSUP=0;EVTYPE=PE;PRIN
+2	109689952	105511	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-5261;END=109695213;STR=+-:161;IMPRECISE;CIPOS=-1,6;CIEND=-4,1;EVENT=105511;SUP=161;PESUP=161;SRSUP=0;EVTYPE=PE;PRIN
+2	114151331	106458	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-2289;END=114153620;STR=+-:175;IMPRECISE;CIPOS=-1,8;CIEND=0,0;EVENT=106458;SUP=175;PESUP=175;SRSUP=0;EVTYPE=PE;PRIN
+2	115628107	106855	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-746;END=115628853;STR=+-:10;CIPOS=0,0;CIEND=0,0;EVENT=106855;SUP=10;PESUP=0;SRSUP=10;EVTYPE=SR;PRIN
+2	116662076	107179	G	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-579;END=116662655;STR=+-:76;CIPOS=0,0;CIEND=0,0;EVENT=107179;SUP=76;PESUP=0;SRSUP=76;EVTYPE=SR;PRIN
+2	119713988	108142	T	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-135;END=119714123;STR=+-:80;CIPOS=0,0;CIEND=0,0;EVENT=108142;SUP=80;PESUP=1;SRSUP=79;EVTYPE=PE,SR;PRIN
+2	122623755	109021	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-53;END=122623808;STR=+-:187;CIPOS=0,0;CIEND=0,0;EVENT=109021;SUP=187;PESUP=1;SRSUP=186;EVTYPE=PE,SR;PRIN
+2	123364878	109241	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-497;END=123365375;STR=+-:729;CIPOS=0,0;CIEND=0,0;EVENT=109241;SUP=729;PESUP=679;SRSUP=50;EVTYPE=PE,SR;PRIN
+2	123476601	109295	T	<INV>	0	.	TOOL=LUMPY;SVTYPE=INV;SVLEN=5903;END=123482504;STR=--:192;CIPOS=0,0;CIEND=0,0;EVENT=109295;SUP=192;PESUP=138;SRSUP=54;EVTYPE=PE,SR;PRIN
+2	125766561	110003	C	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1685;END=125768246;STR=+-:682;CIPOS=0,0;CIEND=0,0;EVENT=110003;SUP=682;PESUP=464;SRSUP=218;EVTYPE=PE,SR;PRIN
+2	126443251	93668	C	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-8579;END=126451830;STR=+-:633;CIPOS=0,0;CIEND=0,0;EVENT=93668;SUP=633;PESUP=454;SRSUP=179;EVTYPE=PE,SR;PRIN
+2	126509720	110262	G	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-881;END=126510601;STR=+-:294;IMPRECISE;CIPOS=0,2;CIEND=-2,0;EVENT=110262;SUP=294;PESUP=293;SRSUP=1;EVTYPE=PE,SR;PRIN
+2	127674758	110619	C	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-2513;END=127677271;STR=+-:1283;CIPOS=0,0;CIEND=0,0;EVENT=110619;SUP=1283;PESUP=934;SRSUP=349;EVTYPE=PE,SR;PRIN
+2	127718904	110632	G	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-3442;END=127722346;STR=+-:13;IMPRECISE;CIPOS=-1,3;CIEND=-3,0;EVENT=110632;SUP=13;PESUP=12;SRSUP=1;EVTYPE=PE,SR;PRIN
+2	129638421	112341	C	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-7781;END=129646202;STR=+-:416;CIPOS=0,0;CIEND=0,0;EVENT=112341;SUP=416;PESUP=393;SRSUP=23;EVTYPE=PE,SR;PRIN
+2	130242246	112548	T	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-9172;END=130251418;STR=+-:137;CIPOS=0,0;CIEND=0,0;EVENT=112548;SUP=137;PESUP=127;SRSUP=10;EVTYPE=PE,SR;PRIN
+2	130954938	110868	T	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-2458;END=130957396;STR=+-:468;IMPRECISE;CIPOS=0,1;CIEND=0,0;EVENT=110868;SUP=468;PESUP=468;SRSUP=0;EVTYPE=PE;PRIN
+2	131886576	112860	T	<INV>	0	.	TOOL=LUMPY;SVTYPE=INV;SVLEN=729;END=131887305;STR=--:450;CIPOS=0,0;CIEND=0,0;EVENT=112860;SUP=450;PESUP=262;SRSUP=188;EVTYPE=PE,SR;PRIN
+2	133671869	113192	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-2619;END=133674488;STR=+-:73;IMPRECISE;CIPOS=0,24;CIEND=-46,1;EVENT=113192;SUP=73;PESUP=73;SRSUP=0;EVTYPE=PE;PRIN
+2	138490122	114755	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-369;END=138490491;STR=+-:300;CIPOS=0,0;CIEND=0,0;EVENT=114755;SUP=300;PESUP=213;SRSUP=87;EVTYPE=PE,SR;PRIN
+2	146842404	117708	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-144;END=146842548;STR=+-:50;CIPOS=0,0;CIEND=0,0;EVENT=117708;SUP=50;PESUP=0;SRSUP=50;EVTYPE=SR;PRIN
+2	146862617	117717	C	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-14244;END=146876861;STR=+-:874;CIPOS=0,0;CIEND=0,0;EVENT=117717;SUP=874;PESUP=621;SRSUP=253;EVTYPE=PE,SR;PRIN
+2	151031138	119079	T	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-7107;END=151038245;STR=+-:364;CIPOS=0,0;CIEND=0,0;EVENT=119079;SUP=364;PESUP=269;SRSUP=95;EVTYPE=PE,SR;PRIN
+2	152041205	119412	T	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-286;END=152041491;STR=+-:175;CIPOS=0,0;CIEND=0,0;EVENT=119412;SUP=175;PESUP=4;SRSUP=171;EVTYPE=PE,SR;PRIN
+2	154494935	120211	A	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-216;END=154495151;STR=+-:392;CIPOS=0,0;CIEND=0,0;EVENT=120211;SUP=392;PESUP=66;SRSUP=326;EVTYPE=PE,SR;PRIN
+2	154895771	120337	G	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-3406;END=154899177;STR=+-:209;CIPOS=0,0;CIEND=0,0;EVENT=120337;SUP=209;PESUP=177;SRSUP=32;EVTYPE=PE,SR;PRIN
+2	159644059	121948	C	<DEL>	0	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-59;END=159644118;STR=+-:123;CIPOS=0,0;CIEND=0,0;EVENT=121948;SUP=123;PESUP=0;SRSUP=123;EVTYPE=SR;PRIN
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