feat: implement ingest and aggregate for sniffles2 (#296) (#312)

README.md

@@ -162,6 +162,7 @@ The command supports the following variant callers and can guess the caller from
 - Manta
 - MELT
 - PopDel
+- Sniffles2
 
 One record will be written out for each variant, each with a single alternate allele.
 

src/strucvars/ingest/header.rs

@@ -293,6 +293,7 @@ mod test {
     #[case("tests/strucvars/ingest/manta-min.vcf")]
     #[case("tests/strucvars/ingest/melt-min.vcf")]
     #[case("tests/strucvars/ingest/popdel-min.vcf")]
+    #[case("tests/strucvars/ingest/sniffles2-min.vcf")]
     #[tokio::test]
     async fn build_output_header_37(#[case] path: &str) -> Result<(), anyhow::Error> {
         mehari::common::set_snapshot_suffix!("{}", path.split('/').last().unwrap());
@@ -338,6 +339,7 @@ mod test {
     #[case("tests/strucvars/ingest/manta-min.vcf")]
     #[case("tests/strucvars/ingest/melt-min.vcf")]
     #[case("tests/strucvars/ingest/popdel-min.vcf")]
+    #[case("tests/strucvars/ingest/sniffles2-min.vcf")]
     #[tokio::test]
     async fn build_output_header_38(#[case] path: &str) -> Result<(), anyhow::Error> {
         mehari::common::set_snapshot_suffix!("{}", path.split('/').last().unwrap());

src/strucvars/ingest/mod.rs

@@ -230,6 +230,8 @@ async fn write_ingest_record(
             Ok(Some("Popdel".to_string()))
         } else if caller.starts_with("MELTv") {
             Ok(Some("Melt".to_string()))
+        } else if caller.starts_with("SNIFFLESv") {
+            Ok(Some("Sniffles".to_string()))
         } else {
             anyhow::bail!("unknown caller: {}", caller)
         }
@@ -486,6 +488,7 @@ mod test {
                 String::from("tests/strucvars/ingest/gcnv-min.vcf"),
                 String::from("tests/strucvars/ingest/manta-min.vcf"),
                 String::from("tests/strucvars/ingest/melt-min.vcf"),
+                String::from("tests/strucvars/ingest/sniffles2-min.vcf"),
             ],
             path_cov_vcf: vec![],
             path_ped: "tests/strucvars/ingest/dragen-cnv-min.ped".into(),
@@ -558,6 +561,7 @@ mod test {
                 String::from("tests/strucvars/ingest/gcnv-min.vcf.gz"),
                 String::from("tests/strucvars/ingest/manta-min.vcf.gz"),
                 String::from("tests/strucvars/ingest/melt-min.vcf.gz"),
+                String::from("tests/strucvars/ingest/sniffles2-min.vcf.gz"),
             ],
             path_cov_vcf: vec![],
             path_ped: "tests/strucvars/ingest/dragen-cnv-min.ped".into(),

src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@sniffles2-min.vcf.snap

@@ -0,0 +1,62 @@
+---
+source: src/strucvars/ingest/header.rs
+expression: "std::fs::read_to_string(out_path_str)?"
+---
+##fileformat=VCFv4.4
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the longest variant described in this record">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant">
+##INFO=<ID=SVCLAIM,Number=A,Type=String,Description="Claim made by the structural variant call. Valid values are D, J, DJ for abundance, adjacency and both respectively">
+##INFO=<ID=callers,Number=.,Type=String,Description="Callers that called the variant">
+##INFO=<ID=chr2,Number=1,Type=String,Description="Second chromosome, if not equal to CHROM">
+##INFO=<ID=annsv,Number=1,Type=String,Description="Effect annotations: 'Allele | Annotation | Gene_Name | Gene_ID'">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=pec,Number=1,Type=Integer,Description="Total coverage with paired-end reads">
+##FORMAT=<ID=pev,Number=1,Type=Integer,Description="Paired-end reads supporting the variant">
+##FORMAT=<ID=src,Number=1,Type=Integer,Description="Total coverage with split reads">
+##FORMAT=<ID=srv,Number=1,Type=Integer,Description="Split reads supporting the variant">
+##FORMAT=<ID=amq,Number=1,Type=Float,Description="Average mapping quality over the variant">
+##FORMAT=<ID=cn,Number=1,Type=Integer,Description="Copy number of the variant in the sample">
+##FORMAT=<ID=anc,Number=1,Type=Float,Description="Average normalized coverage over the variant in the sample">
+##FORMAT=<ID=pc,Number=1,Type=Integer,Description="Point count (windows/targets/probes)">
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=DUP,Description="Duplication">
+##ALT=<ID=INS,Description="Insertion">
+##ALT=<ID=CNV,Description="Copy Number Variation">
+##ALT=<ID=INV,Description="Inversion">
+##contig=<ID=1,length=249250621,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=2,length=243199373,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=3,length=198022430,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=4,length=191154276,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=5,length=180915260,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=6,length=171115067,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=7,length=159138663,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=8,length=146364022,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=9,length=141213431,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=10,length=135534747,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=11,length=135006516,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=12,length=133851895,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=13,length=115169878,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=14,length=107349540,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=15,length=102531392,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=16,length=90354753,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=17,length=81195210,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=18,length=78077248,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=19,length=59128983,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=20,length=63025520,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=21,length=48129895,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=22,length=51304566,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=X,length=155270560,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=Y,length=59373566,assembly="GRCh37",species="Homo sapiens">
+##contig=<ID=MT,length=16569,assembly="GRCh37",species="Homo sapiens">
+##fileDate=20230421
+##x-varfish-genome-build=GRCh37
+##SAMPLE=<ID=SAMPLE,Sex="Male",Disease="Affected">
+##PEDIGREE=<ID=SAMPLE>
+##x-varfish-case-uuid=d2bad2ec-a75d-44b9-bd0a-83a3f1331b7c
+##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
+##x-varfish-version=<ID=Sniffles2,Name="Sniffles2",Version="2.2">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE

src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@sniffles2-min.vcf.snap

@@ -0,0 +1,62 @@
+---
+source: src/strucvars/ingest/header.rs
+expression: "std::fs::read_to_string(out_path_str)?"
+---
+##fileformat=VCFv4.4
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the longest variant described in this record">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant">
+##INFO=<ID=SVCLAIM,Number=A,Type=String,Description="Claim made by the structural variant call. Valid values are D, J, DJ for abundance, adjacency and both respectively">
+##INFO=<ID=callers,Number=.,Type=String,Description="Callers that called the variant">
+##INFO=<ID=chr2,Number=1,Type=String,Description="Second chromosome, if not equal to CHROM">
+##INFO=<ID=annsv,Number=1,Type=String,Description="Effect annotations: 'Allele | Annotation | Gene_Name | Gene_ID'">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=pec,Number=1,Type=Integer,Description="Total coverage with paired-end reads">
+##FORMAT=<ID=pev,Number=1,Type=Integer,Description="Paired-end reads supporting the variant">
+##FORMAT=<ID=src,Number=1,Type=Integer,Description="Total coverage with split reads">
+##FORMAT=<ID=srv,Number=1,Type=Integer,Description="Split reads supporting the variant">
+##FORMAT=<ID=amq,Number=1,Type=Float,Description="Average mapping quality over the variant">
+##FORMAT=<ID=cn,Number=1,Type=Integer,Description="Copy number of the variant in the sample">
+##FORMAT=<ID=anc,Number=1,Type=Float,Description="Average normalized coverage over the variant in the sample">
+##FORMAT=<ID=pc,Number=1,Type=Integer,Description="Point count (windows/targets/probes)">
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=DUP,Description="Duplication">
+##ALT=<ID=INS,Description="Insertion">
+##ALT=<ID=CNV,Description="Copy Number Variation">
+##ALT=<ID=INV,Description="Inversion">
+##contig=<ID=chr1,length=248956422,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr2,length=242193529,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr3,length=198295559,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr4,length=190214555,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr5,length=181538259,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr6,length=170805979,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr7,length=159345973,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr8,length=145138636,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr9,length=138394717,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr10,length=133797422,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr11,length=135086622,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr12,length=133275309,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr13,length=114364328,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr14,length=107043718,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr15,length=101991189,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr16,length=90338345,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr17,length=83257441,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr18,length=80373285,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr19,length=58617616,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr20,length=64444167,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr21,length=46709983,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chr22,length=50818468,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chrX,length=156040895,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chrY,length=57227415,assembly="GRCh38",species="Homo sapiens">
+##contig=<ID=chrM,length=16569,assembly="GRCh38",species="Homo sapiens">
+##fileDate=20230421
+##x-varfish-genome-build=GRCh38
+##SAMPLE=<ID=SAMPLE,Sex="Male",Disease="Affected">
+##PEDIGREE=<ID=SAMPLE>
+##x-varfish-case-uuid=d2bad2ec-a75d-44b9-bd0a-83a3f1331b7c
+##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
+##x-varfish-version=<ID=Sniffles2,Name="Sniffles2",Version="2.2">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE

src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__test__smoke_test_singleton.snap

@@ -63,11 +63,15 @@ expression: "std::fs::read_to_string(&args.path_out)?"
 ##x-varfish-version=<ID=Gcnv,Name="Gcnv",Version="4.3.0.0">
 ##x-varfish-version=<ID=Manta,Name="Manta",Version="1.6.0">
 ##x-varfish-version=<ID=Melt,Name="Melt",Version="2.2.2">
+##x-varfish-version=<ID=Sniffles2,Name="Sniffles2",Version="2.2">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
 1	1000	.	N	<INS>	.	.	SVCLAIM=J;SVTYPE=INS;END=1000;SVLEN=1;callers=Melt	GT:GQ:pec:pev:src:srv:amq:cn:anc:pc	1/1:2:1:1:2:2:.:.:.:.
-1	2000	.	N	<INS>	.	.	SVCLAIM=J;SVTYPE=INS;END=2000;SVLEN=1;callers=Melt	GT:GQ:pec:pev:src:srv:amq:cn:anc:pc	0/0:4:4:0:4:1:.:.:.:.
+1	1000	.	N	<DEL>	.	.	SVCLAIM=DJ;SVTYPE=DEL;END=1049;SVLEN=50;callers=Sniffles	GT:GQ:pec:pev:src:srv:amq:cn:anc:pc	1/1:60:.:.:33:33:.:.:.:.
+1	2000	.	N	<INS>	.	.	SVCLAIM=J;SVTYPE=INS;END=2000;SVLEN=1;callers=Melt	GT:GQ:pec:pev:src:srv:amq:cn:anc:pc	0/0:60:4:0:24:24:.:.:.:.
 1	3000	.	N	<INS>	.	.	SVCLAIM=J;SVTYPE=INS;END=3000;SVLEN=1;callers=Melt	GT:GQ:pec:pev:src:srv:amq:cn:anc:pc	0/0:28:23:0:24:1:.:.:.:.
+1	3000	.	N	<INV>	.	.	SVCLAIM=J;SVTYPE=INV;END=3589;SVLEN=590;callers=Sniffles	GT:GQ:pec:pev:src:srv:amq:cn:anc:pc	0/1:24:.:.:37:10:.:.:.:.
+1	4000	.	N	<DUP>	.	.	SVCLAIM=DJ;SVTYPE=DUP;END=17584;SVLEN=13585;callers=Sniffles	GT:GQ:pec:pev:src:srv:amq:cn:anc:pc	0/1:60:.:.:61:18:.:.:.:.
+1	5000	.	N	N]chrUn_JTFH01000344v1_decoy:679]	.	.	SVCLAIM=J;SVTYPE=BND;END=679;chr2=chrUn_JTFH01000344v1_decoy;callers=Sniffles	GT:GQ:pec:pev:src:srv:amq:cn:anc:pc	0/1:15:.:.:31:8:.:.:.:.
 1	1283844	.	N	<CNV>	.	.	SVCLAIM=D;SVTYPE=CNV;END=1284844;SVLEN=1001;callers=DragenCnv	GT:GQ:pec:pev:src:srv:amq:cn:anc:pc	0/1:.:.:.:.:.:.:1:.:1
 1	1598413	.	N	<DEL>	.	.	SVCLAIM=DJ;SVTYPE=DEL;END=1598580;SVLEN=168;callers=DragenSv	GT:GQ:pec:pev:src:srv:amq:cn:anc:pc	1/1:53:2:2:20:20:.:.:.:.
 1	4124001	.	N	<DEL>	.	.	SVCLAIM=D;SVTYPE=DEL;END=4125000;SVLEN=1000;callers=Gcnv	GT:GQ:pec:pev:src:srv:amq:cn:anc:pc	1:.:.:.:.:.:.:1:.:1
-

tests/strucvars/ingest/sniffles2-min.ped

@@ -0,0 +1 @@
+FAM	SAMPLE	0	0	1	2

tests/strucvars/ingest/sniffles2-min.vcf

@@ -0,0 +1,78 @@
+##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