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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20190823
##reference=GRCh38_full_analysis_set_plus_decoy_hla.fa
##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=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
##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=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants">
##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants">
##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=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants">
##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">
##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">
##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples">
##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=SNAME,Number=.,Type=String,Description="Source sample name">
##INFO=<ID=ALG,Number=1,Type=String,Description="Evidence PDF aggregation algorithm">
##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=SU,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=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
##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=DP,Number=1,Type=Integer,Description="Read depth">
##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=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)">
##smoove_count_stats=16239X1:12295708,26753588,800025,6216842
##bcftools_viewVersion=1.9+htslib-1.9
##smoove_version=0.2.4
##contig=<ID=chr1,length=248956422>
##bcftools_annotateVersion=1.9+htslib-1.9
##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Oz -o 16239X1-smoove.genotyped.vcf.gz; Date=Fri Aug 23 18:11:55 2019
##INFO=<ID=GCF,Number=1,Type=Float,Description="GC-content fraction for the variant region betwee 0 and 1.">
##FORMAT=<ID=DHFC,Number=1,Type=Float,Description="duphold depth fold-change">
##FORMAT=<ID=DHBFC,Number=1,Type=Float,Description="duphold depth fold-change compared to bins with matching GC">
##FORMAT=<ID=DHFFC,Number=1,Type=Float,Description="duphold depth flank fold-change compared to 1000bp left and right of event">
##FORMAT=<ID=DHSP,Number=1,Type=Integer,Description="duphold count of spanning read-pairs">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT tumor
chr1 180214710 1836 N <DEL> 1711.24 . SVTYPE=DEL;SVLEN=-242;END=180214952;STRANDS=+-:16;IMPRECISE;CIPOS=-30,184;CIEND=-241,29;CIPOS95=-12,26;CIEND95=-23,14;SU=16;PE=16;SR=0;SNAME=tow19_tumor:605;ALG=PROD;GCF=0.563786;AN=2;AC=2 GT:GQ:SQ:GL:DP ./.:.:.:.:0
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