##fileformat=VCFv4.2
##fileDate=20180410
##source=svaba run -t /local/2763538/474e3b36be9aba5e893234f2d4891e6e.bam -n /local/2763538/3a27910d544adbeab95b2b73c20ab6e5.bam -G /local/2763538/BWA_DNA_RefSeq_Fasta_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa -p 16 -D /local/2763538/dbsnp_indel.vcf -a DO6350 bwa index /local/2763538/BWA_DNA_RefSeq_Fasta_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa 
##reference=/local/2763538/BWA_DNA_RefSeq_Fasta_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
##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=X,length=155270560>
##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=20,length=63025520>
##contig=<ID=Y,length=59373566>
##contig=<ID=19,length=59128983>
##contig=<ID=22,length=51304566>
##contig=<ID=21,length=48129895>
##contig=<ID=GL000192.1,length=547496>
##contig=<ID=GL000225.1,length=211173>
##contig=<ID=GL000194.1,length=191469>
##contig=<ID=GL000193.1,length=189789>
##contig=<ID=GL000200.1,length=187035>
##contig=<ID=GL000222.1,length=186861>
##contig=<ID=GL000212.1,length=186858>
##contig=<ID=GL000195.1,length=182896>
##contig=<ID=GL000223.1,length=180455>
##contig=<ID=GL000224.1,length=179693>
##contig=<ID=GL000219.1,length=179198>
##contig=<ID=GL000205.1,length=174588>
##contig=<ID=GL000215.1,length=172545>
##contig=<ID=GL000216.1,length=172294>
##contig=<ID=GL000217.1,length=172149>
##contig=<ID=GL000199.1,length=169874>
##contig=<ID=GL000211.1,length=166566>
##contig=<ID=GL000213.1,length=164239>
##contig=<ID=GL000220.1,length=161802>
##contig=<ID=GL000218.1,length=161147>
##contig=<ID=GL000209.1,length=159169>
##contig=<ID=GL000221.1,length=155397>
##contig=<ID=GL000214.1,length=137718>
##contig=<ID=GL000228.1,length=129120>
##contig=<ID=GL000227.1,length=128374>
##contig=<ID=GL000191.1,length=106433>
##contig=<ID=GL000208.1,length=92689>
##contig=<ID=GL000198.1,length=90085>
##contig=<ID=GL000204.1,length=81310>
##contig=<ID=GL000233.1,length=45941>
##contig=<ID=GL000237.1,length=45867>
##contig=<ID=GL000230.1,length=43691>
##contig=<ID=GL000242.1,length=43523>
##contig=<ID=GL000243.1,length=43341>
##contig=<ID=GL000241.1,length=42152>
##contig=<ID=GL000236.1,length=41934>
##contig=<ID=GL000240.1,length=41933>
##contig=<ID=GL000206.1,length=41001>
##contig=<ID=GL000232.1,length=40652>
##contig=<ID=GL000234.1,length=40531>
##contig=<ID=GL000202.1,length=40103>
##contig=<ID=GL000238.1,length=39939>
##contig=<ID=GL000244.1,length=39929>
##contig=<ID=GL000248.1,length=39786>
##contig=<ID=GL000196.1,length=38914>
##contig=<ID=GL000249.1,length=38502>
##contig=<ID=GL000246.1,length=38154>
##contig=<ID=GL000203.1,length=37498>
##contig=<ID=GL000197.1,length=37175>
##contig=<ID=GL000245.1,length=36651>
##contig=<ID=GL000247.1,length=36422>
##contig=<ID=GL000201.1,length=36148>
##contig=<ID=GL000235.1,length=34474>
##contig=<ID=GL000239.1,length=33824>
##contig=<ID=GL000210.1,length=27682>
##contig=<ID=GL000231.1,length=27386>
##contig=<ID=GL000229.1,length=19913>
##contig=<ID=MT,length=16569>
##contig=<ID=GL000226.1,length=15008>
##contig=<ID=GL000207.1,length=4262>
##INFO=<ID=DISC_MAPQ,Number=1,Type=Integer,Description="Mean mapping quality of discordant reads mapped here">
##INFO=<ID=NUMPARTS,Number=1,Type=Integer,Description="If detected with assembly, number of parts the contig maps to. Otherwise 0">
##INFO=<ID=MATEMAPQ,Number=1,Type=Integer,Description="Mapping quality of the partner fragment of the contig">
##INFO=<ID=MATEID,Number=1,Type=String,Description="ID of mate breakends">
##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Mapping quality (BWA-MEM) of this fragement of the contig (-1 if discordant only)">
##INFO=<ID=REPSEQ,Number=1,Type=String,Description="Repeat sequence near the event">
##INFO=<ID=READNAMES,Number=.,Type=String,Description="IDs of ALT reads">
##INFO=<ID=SCTG,Number=1,Type=String,Description="Identifier for the contig assembled by svaba to make the SV call">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=BX,Number=.,Type=String,Description="Table of BX tag counts for supporting reads">
##INFO=<ID=NM,Number=1,Type=Integer,Description="Number of mismatches of this alignment fragment to reference">
##INFO=<ID=MATENM,Number=1,Type=Integer,Description="Number of mismatches of partner alignment fragment to reference">
##INFO=<ID=SPAN,Number=1,Type=Integer,Description="Distance between the breakpoints. -1 for interchromosomal">
##INFO=<ID=INSERTION,Number=1,Type=String,Description="Sequence insertion at the breakpoint.">
##INFO=<ID=SUBN,Number=1,Type=Integer,Description="Number of secondary alignments associated with this contig fragment">
##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
##INFO=<ID=HOMSEQ,Number=1,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints. Plus strand sequence displayed.">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=EVDNC,Number=1,Type=String,Description="Evidence for variant. ASSMB assembly only, ASDIS assembly+discordant. DSCRD discordant only, TSI_L templated-sequence insertion (local, e.g. AB or BC of an ABC), TSI_G global (e.g. AC of ABC)">
##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="SV calls comes from a secondary alignment">
##FILTER=<ID=PASS,Description="Strong assembly support, strong discordant support, or combined support. Strong MAPQ">
##FILTER=<ID=TOOSHORT,Description="Contig alignment for part of this rearrangement has <= 25bp match to reference">
##FILTER=<ID=LOWICSUPPORT,Description="Less than 60bp of contig match on one end of an inter-chromosomal break">
##FILTER=<ID=LOWSPLITSMALL,Description="Fewer than 4 split reads for small events ( < 1500 bp)">
##FILTER=<ID=LOWMAPQDISC,Description="Both clusters of reads failed to achieve mean mapq of > 30 for DSCRD">
##FILTER=<ID=LOWAS,Description="Alignment score of one end is less than 80% of contig length, or number of mismatch bases (NM) on one end is >= 10">
##FILTER=<ID=NOLOCAL,Description="Contig realigned to region outside of local assembly region, and no disc support.">
##FILTER=<ID=WEAKDISC,Description="Fewer than 7 supporting discordant reads and no assembly support">
##FILTER=<ID=WEAKSUPPORTHIREP,Description="Fewer then 7 split reads for variant with >= 10 bases of repeat sequence (need to be more strict)">
##FILTER=<ID=LOCALMATCH,Description="Contig realigned to assembly region without clipping">
##FILTER=<ID=LOWSUPPORT,Description="Fewer than 2 split reads or < 4 total alt reads for ASDISC">
##FILTER=<ID=LOWQINVERSION,Description="Assembly-only inversion of span < 300 and < 6 split reads. Common artifact in Illumina data">
##FILTER=<ID=HIGHHOMOLOGY,Description="Contig realigns with > 25% of readlength of homology. High probaility of assembly/mapping artifact">
##FILTER=<ID=NODISC,Description="Rearrangement was not detected independently by assembly">
##FILTER=<ID=DUPREADS,Description="Contig built from what appear to be duplicate reads (split reads all same contig cov))">
##FILTER=<ID=LOWSPANDSCRD,Description="Discordant-only cluster is too small given isize distribution to call confidently">
##FILTER=<ID=COMPETEDISC,Description="Discordant cluster found with nearly same breakpoints, but different strands for DSCRD event">
##FILTER=<ID=MULTIMATCH,Description="Low MAPQ and this contig fragment maps well to multiple locations">
##FILTER=<ID=LOWSPAN,Description="Discordant read cluster (no split read support), and less than 10kb span and < 12 reads">
##FILTER=<ID=SINGLEBX,Description="Variant is supported by only a single BX tag (if run with 10X Genomics data)">
##FILTER=<ID=SIMPLESEQUENCE,Description="Major portion of one contig mapping falls in a simple sequence, as given by -R flag. Assembly-only filter">
##FILTER=<ID=LOWMAPQ,Description="Assembly contig has non 60/60 mapq and no discordant support">
##FORMAT=<ID=LR,Number=1,Type=Float,Description="Log-odds that this variant is REF vs AF=0.5">
##FORMAT=<ID=SL,Number=1,Type=Float,Description="Alignment-quality Scaled log-odds, where LO is LO * (MAPQ - 2*NM)/60">
##FORMAT=<ID=DR,Number=1,Type=Integer,Description="Number of discordant-supported reads for this variant">
##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of spanning reads for this variants">
##FORMAT=<ID=PL,Number=.,Type=Float,Description="Normalized likelihood of the current genotype">
##FORMAT=<ID=GQ,Number=1,Type=String,Description="Genotype quality (currently not supported. Always 0)">
##FORMAT=<ID=LO,Number=1,Type=Float,Description="Log-odds that this variant is real vs artifact">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth of coverage: Number of reads covering site.">
##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Allele depth: Number of reads supporting the variant">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Most likely genotype">
##SAMPLE=<ID=/local/2763538/474e3b36be9aba5e893234f2d4891e6e.bam>
##SAMPLE=<ID=/local/2763538/3a27910d544adbeab95b2b73c20ab6e5.bam>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	/local/2763538/3a27910d544adbeab95b2b73c20ab6e5.bam	/local/2763538/474e3b36be9aba5e893234f2d4891e6e.bam