##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=Jan 10, 2023, 7:53:31 AM
##source=MELTv2.2.2
##reference=hs37d5.fa
##ALT=<ID=INS:ME:ALU,Description="Insertion of ALU element">
##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=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=21,length=48129895>
##contig=<ID=22,length=51304566>
##INFO=<ID=ASSESS,Number=1,Type=Integer,Description="Provides information on evidence availible to decide insertion site.0 = No overlapping reads at site;1 = Imprecise breakpoint due to greater than expected distance between evidence;2 = discordant pair evidence only -- No split read information;3 = left side TSD evidence only;4 = right side TSD evidence only;5 = TSD decided with split reads, highest possible quality">
##INFO=<ID=TSD,Number=1,Type=String,Description="Precise Target Site Duplication for bases, if unknown, value will be NULL">
##INFO=<ID=INTERNAL,Number=2,Type=String,Description="If insertion internal or close to a gene, listed here followed by a discriptor of the location in the gene (either INTRON, EXON_#, 5_UTR, 3_UTR, PROMOTER, or TERMINATOR). If multiple genes intersected, will be separated by '\\|'">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles; If unknown, will be -1">
##INFO=<ID=MEINFO,Number=4,Type=String,Description="Mobile element info of the form NAME,START,END,POLARITY; If START or END is unknown, will be -1; If POLARITY is unknown, will be 'null'">
##INFO=<ID=DIFF,Number=.,Type=String,Description="Coverage and Differences in relation to the ALU reference. Form is %2XCoverage:Differences, with differences delimited by ','">
##INFO=<ID=LP,Number=1,Type=Integer,Description="Total number of discordant pairs supporting the left side of the breakpont">
##INFO=<ID=RP,Number=1,Type=Integer,Description="Total number of discordant pairs supporting the right side of the breakpont">
##INFO=<ID=RA,Number=1,Type=Float,Description="Ratio between LP and RP, reported as log2(LP / RP)">
##INFO=<ID=PRIOR,Number=1,Type=String,Description="True if this site was not discovered in this dataset, but was included on a provided priors list">
##INFO=<ID=SR,Number=1,Type=Integer,Description="Total number of SRs at the estimated breakpoint for this site. Recomended to filter sites with <= 2 SRs">
##FILTER=<ID=s25,Description="Greater than 100.0% of samples do not have data">
##FILTER=<ID=rSD,Description="Ratio of LP to RP is greater than 2.0 standard deviations">
##FILTER=<ID=hDP,Description="More than the expected number of discordant pairs at this site are also split">
##FILTER=<ID=ac0,Description="No individuals in this VCF file were identified with this insertion">
##FILTER=<ID=lc,Description="MEI is embeded in a low complexity region">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GL,Number=3,Type=Float,Description="Genotype likelihood">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Number of ALT reads">
##ALT=<ID=INS:ME:LINE1,Description="Insertion of LINE1 element">
##INFO=<ID=ISTP,Number=1,Type=Integer,Description="Will be approximate location of twin priming breakpoint in relation to L1 reference; 0 if not twin primed; -1 if no measurement">
##ALT=<ID=INS:ME:SVA,Description="Insertion of SVA element">
##contig=<ID=19,length=59128983>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
1	1000	.	T	<INS:ME:ALU>	.	PASS	TSD=null;ASSESS=0;INTERNAL=null,null;SVTYPE=ALU;SVLEN=279;MEINFO=AluYa5,1,280,+;DIFF=0.53:t89c,g90a,c96a,g145a,c174t,g237c;LP=2;RP=1;RA=1;PRIOR=false;SR=0	GT:GL:DP:AD	1/1:-30,-1.81,-0:3:3
1	2000	.	C	<INS:ME:SVA>	.	lc;ac0	TSD=null;ASSESS=2;INTERNAL=null,null;SVTYPE=SVA;SVLEN=1240;MEINFO=SVA,75,1315,-;DIFF=0.1:n1-74,a78c,c126t,c158t,a167g,g192c,t193c,n201-1316;LP=6;RP=1;RA=2.585;PRIOR=false;SR=0	GT:GL:DP:AD	0/0:-0.6,-4.82,-84.6:8:1
1	3000	.	A	<INS:ME:LINE1>	.	ac0	TSD=null;ASSESS=3;INTERNAL=NM_014813,INTRONIC;SVTYPE=LINE1;SVLEN=121;MEINFO=L1Ambig,5897,6018,+;DIFF=0.01:n1-5896,t5901c,a5929g,c5930a,a5931g,a5989t,n5996-6019;LP=10;RP=1;RA=3.322;ISTP=0;PRIOR=false;SR=1	GT:GL:DP:AD	0/0:-0.6,-28.3,-545.8:47:1