Mercurial > repos > hepcat72 > svtyper
changeset 0:00cab3d2e98b draft
planemo upload
| author | hepcat72 |
|---|---|
| date | Wed, 15 Aug 2018 15:40:54 -0400 |
| parents | |
| children | 2ba5317566c0 |
| files | svtyper.xml test-data/out.vcf test-data/test1.bam test-data/test1.bam.bai test-data/test1.bam.json test-data/test1.out.vcf test-data/test1.vcf |
| diffstat | 7 files changed, 2106 insertions(+), 0 deletions(-) [+] |
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--- /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>
--- /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=GL000235.1,length=34474> +##contig=<ID=GL000201.1,length=36148> +##contig=<ID=GL000247.1,length=36422> +##contig=<ID=GL000245.1,length=36651> +##contig=<ID=GL000197.1,length=37175> +##contig=<ID=GL000203.1,length=37498> +##contig=<ID=GL000246.1,length=38154> +##contig=<ID=GL000249.1,length=38502> +##contig=<ID=GL000196.1,length=38914> +##contig=<ID=GL000248.1,length=39786> +##contig=<ID=GL000244.1,length=39929> +##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> +##contig=<ID=GL000241.1,length=42152> +##contig=<ID=GL000243.1,length=43341> +##contig=<ID=GL000242.1,length=43523> +##contig=<ID=GL000230.1,length=43691> +##contig=<ID=GL000237.1,length=45867> +##contig=<ID=GL000233.1,length=45941> +##contig=<ID=GL000204.1,length=81310> 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+##contig=<ID=GL000194.1,length=191469> +##contig=<ID=GL000225.1,length=211173> +##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 . 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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 ./. +2 51926587 88990 A <DEL> 0.00 . 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 ./. +2 51973823 89011 A <DEL> 0.00 . 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 ./. +2 52749686 89272 A <DEL> 0.00 . 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 ./. +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 ./. +2 54565493 89901 G <DEL> 0.00 . 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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 ./. +15 89212842 894054_2 C C]2:84728755] 0.00 . 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 ./.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.bam.json Wed Aug 15 15:40:54 2018 -0400 @@ -0,0 +1,808 @@ +{ + "NA12878": { + "unmapped": 10201896, + "mapped": 1568288008, + "bam": "/gscmnt/gc2802/halllab/sv_aggregate/MISC/realigned_BAMs/NA12878/NA12878.bam", + "libraryArray": [ + { + "library_name": "", + "prevalence": 1.0, + "read_length": 101, + "readgroups": [ + "NA12878.S1" + ], + "histogram": { + "2": 1, + "4": 2, + "5": 3, + "6": 4, + "7": 2, + "8": 10, + "9": 19, + "10": 16, + "11": 17, + "12": 22, + "13": 28, + "14": 31, + "15": 18, + "16": 17, + "17": 21, + "18": 21, + "19": 155, + "20": 233, + "21": 26, + "22": 44, + "23": 44, + "24": 39, + "25": 47, + "26": 43, + "27": 30, + "28": 51, + "29": 35, + "30": 42, + "31": 32, + "32": 36, + "33": 75, + "34": 34, + "35": 63, + "36": 51, + "37": 63, + "38": 55, + "39": 43, + "40": 68, + "41": 72, + "42": 60, + "43": 63, + "44": 74, + "45": 64, + "46": 77, + "47": 112, + "48": 73, + "49": 95, + "50": 96, + "51": 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"789": 2, + "792": 3, + "3": 2, + "656": 4, + "699": 2, + "709": 2, + "733": 3, + "734": 6, + "761": 5, + "757": 1, + "702": 1, + "704": 3, + "715": 5, + "790": 1 + }, + "mean": 320.0287878620012, + "sd": 80.21936446609676 + } + ], + "sample_name": "NA12878" + } +} \ No newline at end of file
--- /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"> 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+##contig=<ID=GL000194.1,length=191469> +##contig=<ID=GL000225.1,length=211173> +##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 . 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TOOL=LUMPY;SVTYPE=DEL;SVLEN=-124;END=144693235;STR=+-:129;CIPOS=0,0;CIEND=0,0;EVENT=198155;SUP=129;PESUP=3;SRSUP=126;EVTYPE=PE,SR;PRIN GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:165:55:55:0:0.00:-0,-17,-55:55:0:55:0:0:0:0:0 +3 145644968 198495 T <DEL> 0.00 . TOOL=LUMPY;SVTYPE=DEL;SVLEN=-4220;END=145649188;STR=+-:226;IMPRECISE;CIPOS=-1,4;CIEND=-19,0;EVENT=198495;SUP=226;PESUP=226;SRSUP=0;EVTYPE=PE;PRIN GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:200:168:168:0:0.00:-0,-51,-168:168:0:78:0:0:90:0:0 +3 148729873 199514 T <DEL> 683.25 . TOOL=LUMPY;SVTYPE=DEL;SVLEN=-230;END=148730103;STR=+-:86;CIPOS=0,0;CIEND=0,0;EVENT=199514;SUP=86;PESUP=1;SRSUP=85;EVTYPE=PE,SR;PRIN GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:200:105:70:34:683.25:-72,-4,-44:69:33:31:5:5:38:22:0.32 +3 149268476 199704 A <DEL> 0.00 . TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1669;END=149270145;STR=+-:276;CIPOS=0,0;CIEND=0,0;EVENT=199704;SUP=276;PESUP=192;SRSUP=84;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 +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
--- /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"> +##contig=<ID=1,length=249250621> +##contig=<ID=2,length=243199373> +##contig=<ID=3,length=198022430> +##contig=<ID=4,length=191154276> +##contig=<ID=5,length=180915260> +##contig=<ID=6,length=171115067> +##contig=<ID=7,length=159138663> +##contig=<ID=8,length=146364022> +##contig=<ID=9,length=141213431> +##contig=<ID=10,length=135534747> +##contig=<ID=11,length=135006516> +##contig=<ID=12,length=133851895> +##contig=<ID=13,length=115169878> +##contig=<ID=14,length=107349540> +##contig=<ID=15,length=102531392> +##contig=<ID=16,length=90354753> +##contig=<ID=17,length=81195210> +##contig=<ID=18,length=78077248> +##contig=<ID=19,length=59128983> +##contig=<ID=20,length=63025520> +##contig=<ID=21,length=48129895> +##contig=<ID=22,length=51304566> +##contig=<ID=X,length=155270560> +##contig=<ID=Y,length=59373566> +##contig=<ID=MT,length=16569> +##contig=<ID=GL000207.1,length=4262> +##contig=<ID=GL000226.1,length=15008> +##contig=<ID=GL000229.1,length=19913> +##contig=<ID=GL000231.1,length=27386> +##contig=<ID=GL000210.1,length=27682> +##contig=<ID=GL000239.1,length=33824> +##contig=<ID=GL000235.1,length=34474> +##contig=<ID=GL000201.1,length=36148> +##contig=<ID=GL000247.1,length=36422> +##contig=<ID=GL000245.1,length=36651> +##contig=<ID=GL000197.1,length=37175> +##contig=<ID=GL000203.1,length=37498> +##contig=<ID=GL000246.1,length=38154> +##contig=<ID=GL000249.1,length=38502> +##contig=<ID=GL000196.1,length=38914> +##contig=<ID=GL000248.1,length=39786> +##contig=<ID=GL000244.1,length=39929> +##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> +##contig=<ID=GL000241.1,length=42152> +##contig=<ID=GL000243.1,length=43341> +##contig=<ID=GL000242.1,length=43523> +##contig=<ID=GL000230.1,length=43691> +##contig=<ID=GL000237.1,length=45867> +##contig=<ID=GL000233.1,length=45941> +##contig=<ID=GL000204.1,length=81310> +##contig=<ID=GL000198.1,length=90085> +##contig=<ID=GL000208.1,length=92689> +##contig=<ID=GL000191.1,length=106433> +##contig=<ID=GL000227.1,length=128374> +##contig=<ID=GL000228.1,length=129120> +##contig=<ID=GL000214.1,length=137718> +##contig=<ID=GL000221.1,length=155397> +##contig=<ID=GL000209.1,length=159169> +##contig=<ID=GL000218.1,length=161147> +##contig=<ID=GL000220.1,length=161802> +##contig=<ID=GL000213.1,length=164239> +##contig=<ID=GL000211.1,length=166566> +##contig=<ID=GL000199.1,length=169874> +##contig=<ID=GL000217.1,length=172149> +##contig=<ID=GL000216.1,length=172294> +##contig=<ID=GL000215.1,length=172545> +##contig=<ID=GL000205.1,length=174588> +##contig=<ID=GL000219.1,length=179198> +##contig=<ID=GL000224.1,length=179693> +##contig=<ID=GL000223.1,length=180455> +##contig=<ID=GL000195.1,length=182896> +##contig=<ID=GL000212.1,length=186858> +##contig=<ID=GL000222.1,length=186861> +##contig=<ID=GL000200.1,length=187035> +##contig=<ID=GL000193.1,length=189789> +##contig=<ID=GL000194.1,length=191469> +##contig=<ID=GL000225.1,length=211173> +##contig=<ID=GL000192.1,length=547496> +#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 . 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