From a2dd716a67d60533534269faef8e87e30496bce0 Mon Sep 17 00:00:00 2001
From: Ross Lazarus <fubar2@users.noreply.github.com>
Date: Thu, 14 Nov 2024 18:16:24 +1100
Subject: [PATCH] update sniffles to new 2.5.2 release (#6557)

* update sniffles to new 2.5.2 release

* Update tools/sniffles/sniffles.xml

Co-authored-by: M Bernt <m.bernt@ufz.de>

---------

Co-authored-by: M Bernt <m.bernt@ufz.de>
---
 tools/sniffles/sniffles.xml                    |  4 ++--
 tools/sniffles/test-data/expected_outcome3.vcf | 17 +++++++++--------
 tools/sniffles/test-data/expected_outcome4.vcf | 17 +++++++++--------
 tools/sniffles/test-data/expected_outcome5.vcf | 15 ++++++++-------
 tools/sniffles/test-data/expected_outcome6.vcf | 17 +++++++++--------
 tools/sniffles/test-data/expected_output.vcf   | 17 +++++++++--------
 tools/sniffles/test-data/expected_output2.vcf  | 17 +++++++++--------
 7 files changed, 55 insertions(+), 49 deletions(-)

diff --git a/tools/sniffles/sniffles.xml b/tools/sniffles/sniffles.xml
index ba538bca70e..3046f6b686a 100644
--- a/tools/sniffles/sniffles.xml
+++ b/tools/sniffles/sniffles.xml
@@ -1,7 +1,7 @@
-<tool id="sniffles" name="sniffles" version="@TOOL_VERSION@+galaxy1" profile="23.0">
+<tool id="sniffles" name="sniffles" version="@TOOL_VERSION@+galaxy0" profile="23.0">
     <description>Structural variation caller using third generation sequencing</description>
     <macros>
-        <token name="@TOOL_VERSION@">2.4</token>
+        <token name="@TOOL_VERSION@">2.5.2</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">sniffles</xref>
diff --git a/tools/sniffles/test-data/expected_outcome3.vcf b/tools/sniffles/test-data/expected_outcome3.vcf
index 7e025bfc75a..089184fc5d7 100644
--- a/tools/sniffles/test-data/expected_outcome3.vcf
+++ b/tools/sniffles/test-data/expected_outcome3.vcf
@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.2
-##source=Sniffles2_2.4
-##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/6/outputs/dataset_85e708bb-74e2-4686-8dca-f0e9404b4e44.dat --allow-overwrite --minsupport 1 --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5"
-##fileDate="2024/09/28 23:19:48"
+##source=Sniffles2_2.5
+##command="/home/ross/miniconda3/envs/__sniffles@2.5.2/bin/sniffles -t 1 -i input.bam -v /tmp/tmpqwecq14c/job_working_directory/000/6/outputs/dataset_c8216b3d-5cba-4681-a3da-03306ae2e22a.dat --allow-overwrite --minsupport 1 --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5"
+##fileDate="2024/11/13 10:03:40"
 ##contig=<ID=1,length=249250621>
 ##contig=<ID=2,length=243199373>
 ##contig=<ID=3,length=198022430>
@@ -106,14 +106,15 @@
 ##FILTER=<ID=STDEV_LEN,Description="SV length standard deviation filter">
 ##FILTER=<ID=COV_MIN,Description="Minimum coverage filter">
 ##FILTER=<ID=COV_MIN_GT,Description="Minimum coverage filter (missing genotype)">
-##FILTER=<ID=COV_CHANGE,Description="Coverage change filter">
+##FILTER=<ID=COV_CHANGE_DEL,Description="Coverage change filter for DEL">
+##FILTER=<ID=COV_CHANGE_DUP,Description="Coverage change filter for DUP">
 ##FILTER=<ID=COV_CHANGE_INS,Description="Coverage change filter for INS">
 ##FILTER=<ID=COV_CHANGE_FRAC_US,Description="Coverage fractional change filter: upstream-start">
 ##FILTER=<ID=COV_CHANGE_FRAC_SC,Description="Coverage fractional change filter: start-center">
 ##FILTER=<ID=COV_CHANGE_FRAC_CE,Description="Coverage fractional change filter: center-end">
 ##FILTER=<ID=COV_CHANGE_FRAC_ED,Description="Coverage fractional change filter: end-downstream">
-##FILTER=<ID=MOSAIC_AF,Description="Mosaic variant allele frequency filter">
-##FILTER=<ID=NOT_MOSAIC_AF,Description="Variant allele frequency filter for non-mosaic">
+##FILTER=<ID=MOSAIC_VAF,Description="Mosaic variant allele fraction filter">
+##FILTER=<ID=NOT_MOSAIC_VAF,Description="Variant allele fraction filter for non-mosaic">
 ##FILTER=<ID=ALN_NM,Description="Length adjusted mismatch filter">
 ##FILTER=<ID=STRAND_BND,Description="Strand support filter for BNDs">
 ##FILTER=<ID=STRAND,Description="Strand support filter for germline SVs">
@@ -138,8 +139,8 @@
 ##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=VAF,Number=1,Type=Float,Description="Variant Allele Fraction">
 ##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
-21	21492142	Sniffles2.DEL.0S14	N	<DEL>	52	PASS	PRECISE;SVTYPE=DEL;SVLEN=-506;END=21492648;SUPPORT=48;COVERAGE=46,43,43,43,48;STRAND=+-;AF=1.000;STDEV_LEN=0.509;STDEV_POS=1.404	GT:GQ:DR:DV	1/1:60:0:48
+21	21492142	Sniffles2.DEL.0S14	N	<DEL>	52	PASS	PRECISE;SVTYPE=DEL;SVLEN=-506;END=21492647;SUPPORT=48;COVERAGE=46,43,43,43,48;STRAND=+-;STDEV_LEN=0.509;STDEV_POS=1.404;VAF=0.527	GT:GQ:DR:DV	0/1:60:43:48
diff --git a/tools/sniffles/test-data/expected_outcome4.vcf b/tools/sniffles/test-data/expected_outcome4.vcf
index fd2cc1d8cc7..146ad613dcd 100644
--- a/tools/sniffles/test-data/expected_outcome4.vcf
+++ b/tools/sniffles/test-data/expected_outcome4.vcf
@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.2
-##source=Sniffles2_2.4
-##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/8/outputs/dataset_76b2ed7a-d091-4613-bda7-505cd86d4277.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 5 --cluster-r 2.5"
-##fileDate="2024/09/28 23:20:28"
+##source=Sniffles2_2.5
+##command="/home/ross/miniconda3/envs/__sniffles@2.5.2/bin/sniffles -t 1 -i input.bam -v /tmp/tmpqwecq14c/job_working_directory/000/8/outputs/dataset_04542ae5-5626-433d-b23d-a820097bb524.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 5 --cluster-r 2.5"
+##fileDate="2024/11/13 10:04:19"
 ##contig=<ID=1,length=249250621>
 ##contig=<ID=2,length=243199373>
 ##contig=<ID=3,length=198022430>
@@ -106,14 +106,15 @@
 ##FILTER=<ID=STDEV_LEN,Description="SV length standard deviation filter">
 ##FILTER=<ID=COV_MIN,Description="Minimum coverage filter">
 ##FILTER=<ID=COV_MIN_GT,Description="Minimum coverage filter (missing genotype)">
-##FILTER=<ID=COV_CHANGE,Description="Coverage change filter">
+##FILTER=<ID=COV_CHANGE_DEL,Description="Coverage change filter for DEL">
+##FILTER=<ID=COV_CHANGE_DUP,Description="Coverage change filter for DUP">
 ##FILTER=<ID=COV_CHANGE_INS,Description="Coverage change filter for INS">
 ##FILTER=<ID=COV_CHANGE_FRAC_US,Description="Coverage fractional change filter: upstream-start">
 ##FILTER=<ID=COV_CHANGE_FRAC_SC,Description="Coverage fractional change filter: start-center">
 ##FILTER=<ID=COV_CHANGE_FRAC_CE,Description="Coverage fractional change filter: center-end">
 ##FILTER=<ID=COV_CHANGE_FRAC_ED,Description="Coverage fractional change filter: end-downstream">
-##FILTER=<ID=MOSAIC_AF,Description="Mosaic variant allele frequency filter">
-##FILTER=<ID=NOT_MOSAIC_AF,Description="Variant allele frequency filter for non-mosaic">
+##FILTER=<ID=MOSAIC_VAF,Description="Mosaic variant allele fraction filter">
+##FILTER=<ID=NOT_MOSAIC_VAF,Description="Variant allele fraction filter for non-mosaic">
 ##FILTER=<ID=ALN_NM,Description="Length adjusted mismatch filter">
 ##FILTER=<ID=STRAND_BND,Description="Strand support filter for BNDs">
 ##FILTER=<ID=STRAND,Description="Strand support filter for germline SVs">
@@ -138,8 +139,8 @@
 ##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=VAF,Number=1,Type=Float,Description="Variant Allele Fraction">
 ##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
-21	21492142	Sniffles2.DEL.1S14	N	<DEL>	52	PASS	PRECISE;SVTYPE=DEL;SVLEN=-506;END=21492648;SUPPORT=47;COVERAGE=48,43,43,43,51;STRAND=+-;AF=1.000;STDEV_LEN=0.500;STDEV_POS=1.384	GT:GQ:DR:DV	1/1:60:0:47
+21	21492142	Sniffles2.DEL.1S14	N	<DEL>	52	PASS	PRECISE;SVTYPE=DEL;SVLEN=-506;END=21492647;SUPPORT=47;COVERAGE=48,43,43,43,51;STRAND=+-;STDEV_LEN=0.500;STDEV_POS=1.384;VAF=0.522	GT:GQ:DR:DV	0/1:60:43:47
diff --git a/tools/sniffles/test-data/expected_outcome5.vcf b/tools/sniffles/test-data/expected_outcome5.vcf
index cd2c7e50003..ce3a4d6a100 100644
--- a/tools/sniffles/test-data/expected_outcome5.vcf
+++ b/tools/sniffles/test-data/expected_outcome5.vcf
@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.2
-##source=Sniffles2_2.4
-##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/10/outputs/dataset_a9aaaabe-54e2-4f60-9a73-0454076bd7c5.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5 --mosaic"
-##fileDate="2024/09/28 23:21:10"
+##source=Sniffles2_2.5
+##command="/home/ross/miniconda3/envs/__sniffles@2.5.2/bin/sniffles -t 1 -i input.bam -v /tmp/tmpqwecq14c/job_working_directory/000/10/outputs/dataset_0e92fd8e-42f6-4ba5-a5f3-5ec578798305.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5 --mosaic"
+##fileDate="2024/11/13 10:05:00"
 ##contig=<ID=1,length=249250621>
 ##contig=<ID=2,length=243199373>
 ##contig=<ID=3,length=198022430>
@@ -106,14 +106,15 @@
 ##FILTER=<ID=STDEV_LEN,Description="SV length standard deviation filter">
 ##FILTER=<ID=COV_MIN,Description="Minimum coverage filter">
 ##FILTER=<ID=COV_MIN_GT,Description="Minimum coverage filter (missing genotype)">
-##FILTER=<ID=COV_CHANGE,Description="Coverage change filter">
+##FILTER=<ID=COV_CHANGE_DEL,Description="Coverage change filter for DEL">
+##FILTER=<ID=COV_CHANGE_DUP,Description="Coverage change filter for DUP">
 ##FILTER=<ID=COV_CHANGE_INS,Description="Coverage change filter for INS">
 ##FILTER=<ID=COV_CHANGE_FRAC_US,Description="Coverage fractional change filter: upstream-start">
 ##FILTER=<ID=COV_CHANGE_FRAC_SC,Description="Coverage fractional change filter: start-center">
 ##FILTER=<ID=COV_CHANGE_FRAC_CE,Description="Coverage fractional change filter: center-end">
 ##FILTER=<ID=COV_CHANGE_FRAC_ED,Description="Coverage fractional change filter: end-downstream">
-##FILTER=<ID=MOSAIC_AF,Description="Mosaic variant allele frequency filter">
-##FILTER=<ID=NOT_MOSAIC_AF,Description="Variant allele frequency filter for non-mosaic">
+##FILTER=<ID=MOSAIC_VAF,Description="Mosaic variant allele fraction filter">
+##FILTER=<ID=NOT_MOSAIC_VAF,Description="Variant allele fraction filter for non-mosaic">
 ##FILTER=<ID=ALN_NM,Description="Length adjusted mismatch filter">
 ##FILTER=<ID=STRAND_BND,Description="Strand support filter for BNDs">
 ##FILTER=<ID=STRAND,Description="Strand support filter for germline SVs">
@@ -138,7 +139,7 @@
 ##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=VAF,Number=1,Type=Float,Description="Variant Allele Fraction">
 ##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
diff --git a/tools/sniffles/test-data/expected_outcome6.vcf b/tools/sniffles/test-data/expected_outcome6.vcf
index f30fa668b4e..c3bef9e38bd 100644
--- a/tools/sniffles/test-data/expected_outcome6.vcf
+++ b/tools/sniffles/test-data/expected_outcome6.vcf
@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.2
-##source=Sniffles2_2.4
-##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/13/outputs/dataset_93c07e69-9ce4-4394-84c8-8a51cb2e2c89.dat --allow-overwrite --reference reference.fa --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5"
-##fileDate="2024/09/28 23:21:51"
+##source=Sniffles2_2.5
+##command="/home/ross/miniconda3/envs/__sniffles@2.5.2/bin/sniffles -t 1 -i input.bam -v /tmp/tmpqwecq14c/job_working_directory/000/13/outputs/dataset_46e2d702-73e3-453f-9f8c-fba7467d34a7.dat --allow-overwrite --reference reference.fa --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5"
+##fileDate="2024/11/13 10:05:40"
 ##contig=<ID=1,length=249250621>
 ##contig=<ID=2,length=243199373>
 ##contig=<ID=3,length=198022430>
@@ -106,14 +106,15 @@
 ##FILTER=<ID=STDEV_LEN,Description="SV length standard deviation filter">
 ##FILTER=<ID=COV_MIN,Description="Minimum coverage filter">
 ##FILTER=<ID=COV_MIN_GT,Description="Minimum coverage filter (missing genotype)">
-##FILTER=<ID=COV_CHANGE,Description="Coverage change filter">
+##FILTER=<ID=COV_CHANGE_DEL,Description="Coverage change filter for DEL">
+##FILTER=<ID=COV_CHANGE_DUP,Description="Coverage change filter for DUP">
 ##FILTER=<ID=COV_CHANGE_INS,Description="Coverage change filter for INS">
 ##FILTER=<ID=COV_CHANGE_FRAC_US,Description="Coverage fractional change filter: upstream-start">
 ##FILTER=<ID=COV_CHANGE_FRAC_SC,Description="Coverage fractional change filter: start-center">
 ##FILTER=<ID=COV_CHANGE_FRAC_CE,Description="Coverage fractional change filter: center-end">
 ##FILTER=<ID=COV_CHANGE_FRAC_ED,Description="Coverage fractional change filter: end-downstream">
-##FILTER=<ID=MOSAIC_AF,Description="Mosaic variant allele frequency filter">
-##FILTER=<ID=NOT_MOSAIC_AF,Description="Variant allele frequency filter for non-mosaic">
+##FILTER=<ID=MOSAIC_VAF,Description="Mosaic variant allele fraction filter">
+##FILTER=<ID=NOT_MOSAIC_VAF,Description="Variant allele fraction filter for non-mosaic">
 ##FILTER=<ID=ALN_NM,Description="Length adjusted mismatch filter">
 ##FILTER=<ID=STRAND_BND,Description="Strand support filter for BNDs">
 ##FILTER=<ID=STRAND,Description="Strand support filter for germline SVs">
@@ -138,8 +139,8 @@
 ##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=VAF,Number=1,Type=Float,Description="Variant Allele Fraction">
 ##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
-21	21492142	Sniffles2.DEL.0S14	N	<DEL>	52	PASS	PRECISE;SVTYPE=DEL;SVLEN=-506;END=21492648;SUPPORT=48;COVERAGE=46,43,43,43,48;STRAND=+-;AF=1.000;STDEV_LEN=0.509;STDEV_POS=1.404	GT:GQ:DR:DV	1/1:60:0:48
+21	21492142	Sniffles2.DEL.0S14	N	<DEL>	52	PASS	PRECISE;SVTYPE=DEL;SVLEN=-506;END=21492647;SUPPORT=48;COVERAGE=46,43,43,43,48;STRAND=+-;STDEV_LEN=0.509;STDEV_POS=1.404;VAF=0.527	GT:GQ:DR:DV	0/1:60:43:48
diff --git a/tools/sniffles/test-data/expected_output.vcf b/tools/sniffles/test-data/expected_output.vcf
index 4248228b629..53a02d6022e 100644
--- a/tools/sniffles/test-data/expected_output.vcf
+++ b/tools/sniffles/test-data/expected_output.vcf
@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.2
-##source=Sniffles2_2.4
-##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/2/outputs/dataset_c3cc0dff-254a-4e6b-837f-fa8a4db7f051.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --detect-large-ins 0 --cluster-binsize 100 --cluster-r 2.5"
-##fileDate="2024/09/28 23:18:28"
+##source=Sniffles2_2.5
+##command="/home/ross/miniconda3/envs/__sniffles@2.5.2/bin/sniffles -t 1 -i input.bam -v /tmp/tmpqwecq14c/job_working_directory/000/2/outputs/dataset_f00803e7-8823-4f78-8533-432f90cf6d14.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --detect-large-ins 0 --cluster-binsize 100 --cluster-r 2.5"
+##fileDate="2024/11/13 10:02:22"
 ##contig=<ID=1,length=249250621>
 ##contig=<ID=2,length=243199373>
 ##contig=<ID=3,length=198022430>
@@ -106,14 +106,15 @@
 ##FILTER=<ID=STDEV_LEN,Description="SV length standard deviation filter">
 ##FILTER=<ID=COV_MIN,Description="Minimum coverage filter">
 ##FILTER=<ID=COV_MIN_GT,Description="Minimum coverage filter (missing genotype)">
-##FILTER=<ID=COV_CHANGE,Description="Coverage change filter">
+##FILTER=<ID=COV_CHANGE_DEL,Description="Coverage change filter for DEL">
+##FILTER=<ID=COV_CHANGE_DUP,Description="Coverage change filter for DUP">
 ##FILTER=<ID=COV_CHANGE_INS,Description="Coverage change filter for INS">
 ##FILTER=<ID=COV_CHANGE_FRAC_US,Description="Coverage fractional change filter: upstream-start">
 ##FILTER=<ID=COV_CHANGE_FRAC_SC,Description="Coverage fractional change filter: start-center">
 ##FILTER=<ID=COV_CHANGE_FRAC_CE,Description="Coverage fractional change filter: center-end">
 ##FILTER=<ID=COV_CHANGE_FRAC_ED,Description="Coverage fractional change filter: end-downstream">
-##FILTER=<ID=MOSAIC_AF,Description="Mosaic variant allele frequency filter">
-##FILTER=<ID=NOT_MOSAIC_AF,Description="Variant allele frequency filter for non-mosaic">
+##FILTER=<ID=MOSAIC_VAF,Description="Mosaic variant allele fraction filter">
+##FILTER=<ID=NOT_MOSAIC_VAF,Description="Variant allele fraction filter for non-mosaic">
 ##FILTER=<ID=ALN_NM,Description="Length adjusted mismatch filter">
 ##FILTER=<ID=STRAND_BND,Description="Strand support filter for BNDs">
 ##FILTER=<ID=STRAND,Description="Strand support filter for germline SVs">
@@ -138,8 +139,8 @@
 ##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=VAF,Number=1,Type=Float,Description="Variant Allele Fraction">
 ##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
-21	21492142	Sniffles2.DEL.0S14	N	<DEL>	52	PASS	PRECISE;SVTYPE=DEL;SVLEN=-506;END=21492648;SUPPORT=48;COVERAGE=46,43,43,43,48;STRAND=+-;AF=1.000;STDEV_LEN=0.509;STDEV_POS=1.404	GT:GQ:DR:DV	1/1:60:0:48
+21	21492142	Sniffles2.DEL.0S14	N	<DEL>	52	PASS	PRECISE;SVTYPE=DEL;SVLEN=-506;END=21492647;SUPPORT=48;COVERAGE=46,43,43,43,48;STRAND=+-;STDEV_LEN=0.509;STDEV_POS=1.404;VAF=0.527	GT:GQ:DR:DV	0/1:60:43:48
diff --git a/tools/sniffles/test-data/expected_output2.vcf b/tools/sniffles/test-data/expected_output2.vcf
index 912799f5f9d..2088e705f6c 100644
--- a/tools/sniffles/test-data/expected_output2.vcf
+++ b/tools/sniffles/test-data/expected_output2.vcf
@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.2
-##source=Sniffles2_2.4
-##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/4/outputs/dataset_02006b89-2710-4fcc-9ac1-52a711eebee9.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 0 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5"
-##fileDate="2024/09/28 23:19:08"
+##source=Sniffles2_2.5
+##command="/home/ross/miniconda3/envs/__sniffles@2.5.2/bin/sniffles -t 1 -i input.bam -v /tmp/tmpqwecq14c/job_working_directory/000/4/outputs/dataset_d0a9862a-7719-41bc-a0d6-509dc816a92b.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 0 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5"
+##fileDate="2024/11/13 10:03:01"
 ##contig=<ID=1,length=249250621>
 ##contig=<ID=2,length=243199373>
 ##contig=<ID=3,length=198022430>
@@ -106,14 +106,15 @@
 ##FILTER=<ID=STDEV_LEN,Description="SV length standard deviation filter">
 ##FILTER=<ID=COV_MIN,Description="Minimum coverage filter">
 ##FILTER=<ID=COV_MIN_GT,Description="Minimum coverage filter (missing genotype)">
-##FILTER=<ID=COV_CHANGE,Description="Coverage change filter">
+##FILTER=<ID=COV_CHANGE_DEL,Description="Coverage change filter for DEL">
+##FILTER=<ID=COV_CHANGE_DUP,Description="Coverage change filter for DUP">
 ##FILTER=<ID=COV_CHANGE_INS,Description="Coverage change filter for INS">
 ##FILTER=<ID=COV_CHANGE_FRAC_US,Description="Coverage fractional change filter: upstream-start">
 ##FILTER=<ID=COV_CHANGE_FRAC_SC,Description="Coverage fractional change filter: start-center">
 ##FILTER=<ID=COV_CHANGE_FRAC_CE,Description="Coverage fractional change filter: center-end">
 ##FILTER=<ID=COV_CHANGE_FRAC_ED,Description="Coverage fractional change filter: end-downstream">
-##FILTER=<ID=MOSAIC_AF,Description="Mosaic variant allele frequency filter">
-##FILTER=<ID=NOT_MOSAIC_AF,Description="Variant allele frequency filter for non-mosaic">
+##FILTER=<ID=MOSAIC_VAF,Description="Mosaic variant allele fraction filter">
+##FILTER=<ID=NOT_MOSAIC_VAF,Description="Variant allele fraction filter for non-mosaic">
 ##FILTER=<ID=ALN_NM,Description="Length adjusted mismatch filter">
 ##FILTER=<ID=STRAND_BND,Description="Strand support filter for BNDs">
 ##FILTER=<ID=STRAND,Description="Strand support filter for germline SVs">
@@ -138,8 +139,8 @@
 ##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=VAF,Number=1,Type=Float,Description="Variant Allele Fraction">
 ##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
-21	21492142	Sniffles2.DEL.0S14	N	<DEL>	52	PASS	PRECISE;SVTYPE=DEL;SVLEN=-506;END=21492648;SUPPORT=48;COVERAGE=46,43,43,43,48;STRAND=+-;AF=1.000;STDEV_LEN=0.509;STDEV_POS=1.404	GT:GQ:DR:DV	1/1:60:0:48
+21	21492142	Sniffles2.DEL.0S14	N	<DEL>	52	PASS	PRECISE;SVTYPE=DEL;SVLEN=-506;END=21492647;SUPPORT=48;COVERAGE=46,43,43,43,48;STRAND=+-;STDEV_LEN=0.509;STDEV_POS=1.404;VAF=0.527	GT:GQ:DR:DV	0/1:60:43:48