##fileformat=VCFv4.2
##source=Sniffles2_2.2
##command="sniffles --input out/SAMPLE.hac.sniffles.snf --vcf SAMPLE.multi.vcf"
##fileDate="2024/02/09 14:19:35"
##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>
##ALT=<ID=INS,Description="Insertion">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=BND,Description="Breakend; Translocation">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
##FORMAT=<ID=DR,Number=1,Type=Integer,Description="Number of reference reads">
##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of variant reads">
##FORMAT=<ID=ID,Number=1,Type=String,Description="Individual sample SV ID for multi-sample output">
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=GT,Description="Genotype filter">
##FILTER=<ID=SUPPORT_MIN,Description="Minimum read support filter">
##FILTER=<ID=STDEV_POS,Description="SV Breakpoint standard deviation filter">
##FILTER=<ID=STDEV_LEN,Description="SV length standard deviation filter">
##FILTER=<ID=COV_MIN,Description="Minimum coverage filter">
##FILTER=<ID=COV_CHANGE,Description="Coverage change filter">
##FILTER=<ID=COV_CHANGE_FRAC,Description="Coverage fractional change filter">
##FILTER=<ID=MOSAIC_AF,Description="Mosaic maximum allele frequency filter">
##FILTER=<ID=ALN_NM,Description="Length adjusted mismatch filter">
##FILTER=<ID=STRAND,Description="Strand support filter">
##FILTER=<ID=SVLEN_MIN,Description="SV length filter">
##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Structural variation with precise breakpoints">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Structural variation with imprecise breakpoints">
##INFO=<ID=MOSAIC,Number=0,Type=Flag,Description="Structural variation classified as putative mosaic">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of structural variation">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variation">
##INFO=<ID=CHR2,Number=1,Type=String,Description="Mate chromsome for BND SVs">
##INFO=<ID=SUPPORT,Number=1,Type=Integer,Description="Number of reads supporting the structural variation">
##INFO=<ID=SUPPORT_INLINE,Number=1,Type=Integer,Description="Number of reads supporting an INS/DEL SV (non-split events only)">
##INFO=<ID=SUPPORT_LONG,Number=1,Type=Integer,Description="Number of soft-clipped reads putatively supporting the long insertion SV">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of structural variation">
##INFO=<ID=STDEV_POS,Number=1,Type=Float,Description="Standard deviation of structural variation start position">
##INFO=<ID=STDEV_LEN,Number=1,Type=Float,Description="Standard deviation of structural variation length">
##INFO=<ID=COVERAGE,Number=.,Type=Float,Description="Coverages near upstream, start, center, end, downstream of structural variation">
##INFO=<ID=STRAND,Number=1,Type=String,Description="Strands of supporting reads for structural variant">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count, summed up over all samples">
##INFO=<ID=SUPP_VEC,Number=1,Type=String,Description="List of read support for all samples">
##INFO=<ID=CONSENSUS_SUPPORT,Number=1,Type=Integer,Description="Number of reads that support the generated insertion (INS) consensus sequence">
##INFO=<ID=RNAMES,Number=.,Type=String,Description="Names of supporting reads (if enabled with --output-rnames)">
##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
##INFO=<ID=NM,Number=.,Type=Float,Description="Mean number of query alignment length adjusted mismatches of supporting reads">
##INFO=<ID=PHASE,Number=.,Type=String,Description="Phasing information derived from supporting reads, represented as list of: HAPLOTYPE,PHASESET,HAPLOTYPE_SUPPORT,PHASESET_SUPPORT,HAPLOTYPE_FILTER,PHASESET_FILTER">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
chr1	1000	Sniffles2.DEL.CM0	N	<DEL>	54	PASS	PRECISE;SVTYPE=DEL;SVLEN=-50;END=1049;SUPPORT=26;COVERAGE=41,41,42,41,39;STRAND=+-;AC=4;STDEV_LEN=23.094;STDEV_POS=2.887;SUPP_VEC=11	GT:GQ:DR:DV:ID	1/1:60:0:33:Sniffles2.DEL.3720S0
chr1	2000	Sniffles2.INS.0M0	N	GTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGAAGACAGTCCCTCTGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGCAGACAGTCCCTCT	56	PASS	IMPRECISE;SVTYPE=INS;SVLEN=118;END=2000;SUPPORT=30;COVERAGE=31,30,30,30,30;STRAND=+-;AC=4;STDEV_LEN=0.000;STDEV_POS=0.000;SUPP_VEC=11	GT:GQ:DR:DV:ID	1/1:60:0:24:Sniffles2.INS.5S0
chr1	3000	Sniffles2.INV.215M0	N	<INV>	59	PASS	PRECISE;SVTYPE=INV;SVLEN=590;END=3589;SUPPORT=16;COVERAGE=39,19,20,20,40;STRAND=-;AC=2;STDEV_LEN=0.000;STDEV_POS=0.000;SUPP_VEC=11	GT:GQ:DR:DV:ID	0/1:24:27:10:Sniffles2.INV.9A95S0
chr1	4000	Sniffles2.DUP.2F0M1	N	<DUP>	60	PASS	PRECISE;SVTYPE=DUP;SVLEN=13584;END=17584;SUPPORT=20;COVERAGE=42,44,70,42,44;STRAND=+-;AC=2;STDEV_LEN=0.000;STDEV_POS=0.000;SUPP_VEC=11	GT:GQ:DR:DV:ID	0/1:60:43:18:Sniffles2.DUP.954CS1
chr1	5000	Sniffles2.BND.FFM0	N	N]chrUn_JTFH01000344v1_decoy:679]	58	PASS	PRECISE;SVTYPE=BND;SUPPORT=7;COVERAGE=44,30,42,42,40;STRAND=+-;AC=1;STDEV_LEN=0.000;STDEV_POS=0.000;SUPP_VEC=11	GT:GQ:DR:DV:ID	0/1:15:23:8:Sniffles2.BND.C83CS0