test v0.2.3

README.md

@@ -51,7 +51,10 @@ The following variant callers are currently supported:
 - [GATK4 Mutect2](https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2)
 - [LUMPY](https://github.com/arq5x/lumpy-sv)
 - [pbsv](https://github.com/PacificBiosciences/pbsv)
+- [Savana](https://github.com/cortes-ciriano-lab/savana)
+- [Severus](https://github.com/KolmogorovLab/Severus)
 - [Sniffles2](https://github.com/fritzsedlazeck/Sniffles)
 - [Strelka2](https://github.com/Illumina/strelka)
 - [SVIM](https://github.com/eldariont/svim)
+- [SVision-pro](https://github.com/songbowang125/SVision-pro)
 

examples/outputs/sample001_savana_sv_breakpoints.tsv

@@ -0,0 +1,13 @@
+variant_id	variant_call_id	sample_id	chromosome_1	position_1	chromosome_2	position_2	variant_type	reference_allele	alternate_allele	source_id	phase_block_id	clone_id	nucleic_acid	variant_calling_method	sequencing_platform	filter	quality_score	precise	variant_subtype	variant_size	reference_allele_read_count	alternate_allele_read_count	total_read_count	alternate_allele_fraction	alternate_allele_read_ids	variant_sequences	tags	attributes	position_1_annotation_annotator	position_1_annotation_annotator_version	position_1_annotation_gene_id	position_1_annotation_gene_id_stable	position_1_annotation_gene_name	position_1_annotation_gene_strand	position_1_annotation_gene_type	position_1_annotation_gene_version	position_1_annotation_region	position_1_annotation_species	position_2_annotation_annotator	position_2_annotation_annotator_version	position_2_annotation_gene_id	position_2_annotation_gene_id_stable	position_2_annotation_gene_name	position_2_annotation_gene_strand	position_2_annotation_gene_type	position_2_annotation_gene_version	position_2_annotation_region	position_2_annotation_species
+1	tumor_dna_savana_1_INS_chr17:7675193_chr17:7675193	tumor	chr17	7675193	chr17	7675193	INS	G	<INS>	sample001			dna	savana	PACBIO	PASS	-1.0	False		60	0	60	60	1.0				ID=ID_3_1;SVTYPE=INS;NORMAL_SUPPORT=0;TUMOUR_SUPPORT=60;SVLEN=60;BP_NOTATION=<INS>;ORIGINATING_CLUSTER=89ba426b4aa246e5a861722db8e7961b;END_CLUSTER=89ba426b4aa246e5a861722db8e7961b;ORIGIN_STARTS_STD_DEV=0.0;ORIGIN_MAPQ_MEAN=60.0;ORIGIN_EVENT_SIZE_STD_DEV=0.0;ORIGIN_EVENT_SIZE_MEDIAN=60.0;ORIGIN_EVENT_SIZE_MEAN=60.0;END_STARTS_STD_DEV=0.0;END_MAPQ_MEAN=60.0;END_EVENT_SIZE_STD_DEV=0.0;END_EVENT_SIZE_MEDIAN=60.0;END_EVENT_SIZE_MEAN=60.0;TUMOUR_DP=60;NORMAL_DP=60;GT=0/1																				
+1	normal_dna_savana_2_INS_chr17:7675193_chr17:7675193	normal	chr17	7675193	chr17	7675193	INS	G	<INS>	sample001			dna	savana	PACBIO	PASS	-1.0	False		60	60	0	60	0.0				ID=ID_3_1;SVTYPE=INS;NORMAL_SUPPORT=0;TUMOUR_SUPPORT=60;SVLEN=60;BP_NOTATION=<INS>;ORIGINATING_CLUSTER=89ba426b4aa246e5a861722db8e7961b;END_CLUSTER=89ba426b4aa246e5a861722db8e7961b;ORIGIN_STARTS_STD_DEV=0.0;ORIGIN_MAPQ_MEAN=60.0;ORIGIN_EVENT_SIZE_STD_DEV=0.0;ORIGIN_EVENT_SIZE_MEDIAN=60.0;ORIGIN_EVENT_SIZE_MEAN=60.0;END_STARTS_STD_DEV=0.0;END_MAPQ_MEAN=60.0;END_EVENT_SIZE_STD_DEV=0.0;END_EVENT_SIZE_MEDIAN=60.0;END_EVENT_SIZE_MEAN=60.0;TUMOUR_DP=60;NORMAL_DP=60;GT=0/1																				
+2	tumor_dna_savana_2_INS_chr17:7676194_chr17:7676194	tumor	chr17	7676194	chr17	7676194	INS	C	<INS>	sample001			dna	savana	PACBIO	PASS	-1.0	False		60	0	60	60	1.0				ID=ID_4_1;SVTYPE=INS;NORMAL_SUPPORT=0;TUMOUR_SUPPORT=60;SVLEN=60;BP_NOTATION=<INS>;ORIGINATING_CLUSTER=db172cd9f5804a2984f266522ac2d258;END_CLUSTER=db172cd9f5804a2984f266522ac2d258;ORIGIN_STARTS_STD_DEV=0.0;ORIGIN_MAPQ_MEAN=60.0;ORIGIN_EVENT_SIZE_STD_DEV=0.0;ORIGIN_EVENT_SIZE_MEDIAN=60.0;ORIGIN_EVENT_SIZE_MEAN=60.0;END_STARTS_STD_DEV=0.0;END_MAPQ_MEAN=60.0;END_EVENT_SIZE_STD_DEV=0.0;END_EVENT_SIZE_MEDIAN=60.0;END_EVENT_SIZE_MEAN=60.0;TUMOUR_DP=60;NORMAL_DP=60;GT=0/1																				
+2	normal_dna_savana_3_INS_chr17:7676194_chr17:7676194	normal	chr17	7676194	chr17	7676194	INS	C	<INS>	sample001			dna	savana	PACBIO	PASS	-1.0	False		60	60	0	60	0.0				ID=ID_4_1;SVTYPE=INS;NORMAL_SUPPORT=0;TUMOUR_SUPPORT=60;SVLEN=60;BP_NOTATION=<INS>;ORIGINATING_CLUSTER=db172cd9f5804a2984f266522ac2d258;END_CLUSTER=db172cd9f5804a2984f266522ac2d258;ORIGIN_STARTS_STD_DEV=0.0;ORIGIN_MAPQ_MEAN=60.0;ORIGIN_EVENT_SIZE_STD_DEV=0.0;ORIGIN_EVENT_SIZE_MEDIAN=60.0;ORIGIN_EVENT_SIZE_MEAN=60.0;END_STARTS_STD_DEV=0.0;END_MAPQ_MEAN=60.0;END_EVENT_SIZE_STD_DEV=0.0;END_EVENT_SIZE_MEDIAN=60.0;END_EVENT_SIZE_MEAN=60.0;TUMOUR_DP=60;NORMAL_DP=60;GT=0/1																				
+3	tumor_dna_savana_3_INS_chr17:7677193_chr17:7677193	tumor	chr17	7677193	chr17	7677193	INS	c	<INS>	sample001			dna	savana	PACBIO	PASS	-1.0	False		60	0	60	60	1.0				ID=ID_5_1;SVTYPE=INS;NORMAL_SUPPORT=0;TUMOUR_SUPPORT=60;SVLEN=60;BP_NOTATION=<INS>;ORIGINATING_CLUSTER=8167f1efa42e46048e24ff6c10fe2447;END_CLUSTER=8167f1efa42e46048e24ff6c10fe2447;ORIGIN_STARTS_STD_DEV=0.0;ORIGIN_MAPQ_MEAN=60.0;ORIGIN_EVENT_SIZE_STD_DEV=0.0;ORIGIN_EVENT_SIZE_MEDIAN=60.0;ORIGIN_EVENT_SIZE_MEAN=60.0;END_STARTS_STD_DEV=0.0;END_MAPQ_MEAN=60.0;END_EVENT_SIZE_STD_DEV=0.0;END_EVENT_SIZE_MEDIAN=60.0;END_EVENT_SIZE_MEAN=60.0;TUMOUR_DP=60;NORMAL_DP=60;GT=0/1																				
+3	normal_dna_savana_4_INS_chr17:7677193_chr17:7677193	normal	chr17	7677193	chr17	7677193	INS	c	<INS>	sample001			dna	savana	PACBIO	PASS	-1.0	False		60	60	0	60	0.0				ID=ID_5_1;SVTYPE=INS;NORMAL_SUPPORT=0;TUMOUR_SUPPORT=60;SVLEN=60;BP_NOTATION=<INS>;ORIGINATING_CLUSTER=8167f1efa42e46048e24ff6c10fe2447;END_CLUSTER=8167f1efa42e46048e24ff6c10fe2447;ORIGIN_STARTS_STD_DEV=0.0;ORIGIN_MAPQ_MEAN=60.0;ORIGIN_EVENT_SIZE_STD_DEV=0.0;ORIGIN_EVENT_SIZE_MEDIAN=60.0;ORIGIN_EVENT_SIZE_MEAN=60.0;END_STARTS_STD_DEV=0.0;END_MAPQ_MEAN=60.0;END_EVENT_SIZE_STD_DEV=0.0;END_EVENT_SIZE_MEDIAN=60.0;END_EVENT_SIZE_MEAN=60.0;TUMOUR_DP=60;NORMAL_DP=60;GT=0/1																				
+4	tumor_dna_savana_4_BND_chr17:7683193_chr17:7683292	tumor	chr17	7683193	chr17	7683292	BND	c	c[chr17:7683292[	sample001			dna	savana	PACBIO	PASS	-1.0	False		100	0	60	60	1.0				ID=ID_0_1;SVTYPE=BND;MATEID=ID_0_2;NORMAL_SUPPORT=0;TUMOUR_SUPPORT=60;SVLEN=99;BP_NOTATION=+-;ORIGINATING_CLUSTER=ddf5b73f483b4a998b2fcbc654bc7921;END_CLUSTER=4ec8c168e1fa4d3584d310023a2d55f2;ORIGIN_STARTS_STD_DEV=0.0;ORIGIN_MAPQ_MEAN=60.0;ORIGIN_EVENT_SIZE_STD_DEV=0.0;ORIGIN_EVENT_SIZE_MEDIAN=99.0;ORIGIN_EVENT_SIZE_MEAN=99.0;END_STARTS_STD_DEV=0.0;END_MAPQ_MEAN=60.0;END_EVENT_SIZE_STD_DEV=0.0;END_EVENT_SIZE_MEDIAN=99.0;END_EVENT_SIZE_MEAN=99.0;TUMOUR_DP=60,60;NORMAL_DP=60,60;GT=0/1																				
+4	normal_dna_savana_5_BND_chr17:7683193_chr17:7683292	normal	chr17	7683193	chr17	7683292	BND	c	c[chr17:7683292[	sample001			dna	savana	PACBIO	PASS	-1.0	False		100	60	0	60	0.0				ID=ID_0_1;SVTYPE=BND;MATEID=ID_0_2;NORMAL_SUPPORT=0;TUMOUR_SUPPORT=60;SVLEN=99;BP_NOTATION=+-;ORIGINATING_CLUSTER=ddf5b73f483b4a998b2fcbc654bc7921;END_CLUSTER=4ec8c168e1fa4d3584d310023a2d55f2;ORIGIN_STARTS_STD_DEV=0.0;ORIGIN_MAPQ_MEAN=60.0;ORIGIN_EVENT_SIZE_STD_DEV=0.0;ORIGIN_EVENT_SIZE_MEDIAN=99.0;ORIGIN_EVENT_SIZE_MEAN=99.0;END_STARTS_STD_DEV=0.0;END_MAPQ_MEAN=60.0;END_EVENT_SIZE_STD_DEV=0.0;END_EVENT_SIZE_MEDIAN=99.0;END_EVENT_SIZE_MEAN=99.0;TUMOUR_DP=60,60;NORMAL_DP=60,60;GT=0/1																				
+6	tumor_dna_savana_5_BND_chr17:7684292_chr17:7684391	tumor	chr17	7684292	chr17	7684391	BND	t	t[chr17:7684391[	sample001			dna	savana	PACBIO	PASS	-1.0	False		100	0	60	60	1.0				ID=ID_1_1;SVTYPE=BND;MATEID=ID_1_2;NORMAL_SUPPORT=0;TUMOUR_SUPPORT=60;SVLEN=99;BP_NOTATION=+-;ORIGINATING_CLUSTER=3c8b6e3f1e1d42bd9b660932ff51b181;END_CLUSTER=26cfdba33d124d7a8d65a702dbb0233f;ORIGIN_STARTS_STD_DEV=0.0;ORIGIN_MAPQ_MEAN=60.0;ORIGIN_EVENT_SIZE_STD_DEV=0.0;ORIGIN_EVENT_SIZE_MEDIAN=99.0;ORIGIN_EVENT_SIZE_MEAN=99.0;END_STARTS_STD_DEV=0.0;END_MAPQ_MEAN=60.0;END_EVENT_SIZE_STD_DEV=0.0;END_EVENT_SIZE_MEDIAN=99.0;END_EVENT_SIZE_MEAN=99.0;TUMOUR_DP=60,60;NORMAL_DP=60,60;GT=0/1																				
+6	normal_dna_savana_6_BND_chr17:7684292_chr17:7684391	normal	chr17	7684292	chr17	7684391	BND	t	t[chr17:7684391[	sample001			dna	savana	PACBIO	PASS	-1.0	False		100	60	0	60	0.0				ID=ID_1_1;SVTYPE=BND;MATEID=ID_1_2;NORMAL_SUPPORT=0;TUMOUR_SUPPORT=60;SVLEN=99;BP_NOTATION=+-;ORIGINATING_CLUSTER=3c8b6e3f1e1d42bd9b660932ff51b181;END_CLUSTER=26cfdba33d124d7a8d65a702dbb0233f;ORIGIN_STARTS_STD_DEV=0.0;ORIGIN_MAPQ_MEAN=60.0;ORIGIN_EVENT_SIZE_STD_DEV=0.0;ORIGIN_EVENT_SIZE_MEDIAN=99.0;ORIGIN_EVENT_SIZE_MEAN=99.0;END_STARTS_STD_DEV=0.0;END_MAPQ_MEAN=60.0;END_EVENT_SIZE_STD_DEV=0.0;END_EVENT_SIZE_MEDIAN=99.0;END_EVENT_SIZE_MEAN=99.0;TUMOUR_DP=60,60;NORMAL_DP=60,60;GT=0/1																				
+8	tumor_dna_savana_6_BND_chr17:7685391_chr17:7685490	tumor	chr17	7685391	chr17	7685490	BND	a	a[chr17:7685490[	sample001			dna	savana	PACBIO	PASS	-1.0	False		100	0	60	60	1.0				ID=ID_2_1;SVTYPE=BND;MATEID=ID_2_2;NORMAL_SUPPORT=0;TUMOUR_SUPPORT=60;SVLEN=99;BP_NOTATION=+-;ORIGINATING_CLUSTER=b4106382726e4724af0ba157d7cbe5a2;END_CLUSTER=200b2dd8e54241bebe846d0a172fed0b;ORIGIN_STARTS_STD_DEV=0.0;ORIGIN_MAPQ_MEAN=60.0;ORIGIN_EVENT_SIZE_STD_DEV=0.0;ORIGIN_EVENT_SIZE_MEDIAN=99.0;ORIGIN_EVENT_SIZE_MEAN=99.0;END_STARTS_STD_DEV=0.0;END_MAPQ_MEAN=60.0;END_EVENT_SIZE_STD_DEV=0.0;END_EVENT_SIZE_MEDIAN=99.0;END_EVENT_SIZE_MEAN=99.0;TUMOUR_DP=60,60;NORMAL_DP=60,60;GT=0/1																				
+8	normal_dna_savana_7_BND_chr17:7685391_chr17:7685490	normal	chr17	7685391	chr17	7685490	BND	a	a[chr17:7685490[	sample001			dna	savana	PACBIO	PASS	-1.0	False		100	60	0	60	0.0				ID=ID_2_1;SVTYPE=BND;MATEID=ID_2_2;NORMAL_SUPPORT=0;TUMOUR_SUPPORT=60;SVLEN=99;BP_NOTATION=+-;ORIGINATING_CLUSTER=b4106382726e4724af0ba157d7cbe5a2;END_CLUSTER=200b2dd8e54241bebe846d0a172fed0b;ORIGIN_STARTS_STD_DEV=0.0;ORIGIN_MAPQ_MEAN=60.0;ORIGIN_EVENT_SIZE_STD_DEV=0.0;ORIGIN_EVENT_SIZE_MEDIAN=99.0;ORIGIN_EVENT_SIZE_MEAN=99.0;END_STARTS_STD_DEV=0.0;END_MAPQ_MEAN=60.0;END_EVENT_SIZE_STD_DEV=0.0;END_EVENT_SIZE_MEDIAN=99.0;END_EVENT_SIZE_MEAN=99.0;TUMOUR_DP=60,60;NORMAL_DP=60,60;GT=0/1																				

examples/outputs/sample001_severus_somatic.tsv

@@ -0,0 +1,6 @@
+variant_id	variant_call_id	sample_id	chromosome_1	position_1	chromosome_2	position_2	variant_type	reference_allele	alternate_allele	source_id	phase_block_id	clone_id	nucleic_acid	variant_calling_method	sequencing_platform	filter	quality_score	precise	variant_subtype	variant_size	reference_allele_read_count	alternate_allele_read_count	total_read_count	alternate_allele_fraction	alternate_allele_read_ids	variant_sequences	tags	attributes	position_1_annotation_annotator	position_1_annotation_annotator_version	position_1_annotation_gene_id	position_1_annotation_gene_id_stable	position_1_annotation_gene_name	position_1_annotation_gene_strand	position_1_annotation_gene_type	position_1_annotation_gene_version	position_1_annotation_region	position_1_annotation_species	position_2_annotation_annotator	position_2_annotation_annotator_version	position_2_annotation_gene_id	position_2_annotation_gene_id_stable	position_2_annotation_gene_name	position_2_annotation_gene_strand	position_2_annotation_gene_type	position_2_annotation_gene_version	position_2_annotation_region	position_2_annotation_species
+1	tumor_dna_severus_1_INS_chr17:7675193_chr17:7675193	tumor	chr17	7675193	chr17	7675193	INS	N	TCATACGTACGATACGATAGCTAGCTACGATGCATATAATCAGCTACAGATCACTAGCTC	sample001			dna	severus	PACBIO	PASS	60.0	True		60	60	60	120	0.5				ID=severus_INS3;PRECISE=True;SVTYPE=INS;SVLEN=60;MAPQ=;GT=0/1;GQ=360;VAF=0.5;hVAF=1.00,0.00,0.00;DR=60;DV=60																				
+2	tumor_dna_severus_2_INS_chr17:7676693_chr17:7676693	tumor	chr17	7676693	chr17	7676693	INS	N	ACGTACAGCTACAGCTACGACTAGCATATAGCTACAGCTACGATCACGTACATAGATAAA	sample001			dna	severus	PACBIO	PASS	60.0	False		60	60	60	120	0.5				ID=severus_INS4;PRECISE=False;SVTYPE=INS;SVLEN=60;MAPQ=;GT=0/1;GQ=360;VAF=0.5;hVAF=1.00,0.00,0.00;DR=60;DV=60																				
+3	tumor_dna_severus_3_DEL_chr17:7683193_chr17:7683293	tumor	chr17	7683193	chr17	7683293	DEL	N	<DEL>	sample001			dna	severus	PACBIO	PASS	60.0	True		100	60	60	120	0.5				ID=severus_DEL0;PRECISE=True;SVTYPE=DEL;SVLEN=100;END=7683293;STRANDS=+-;INSIDE_VNTR=TRUE;MAPQ=;GT=0/1;GQ=360;VAF=0.5;hVAF=1.00,0.00,0.00;DR=60;DV=60																				
+4	tumor_dna_severus_4_DEL_chr17:7684293_chr17:7684393	tumor	chr17	7684293	chr17	7684393	DEL	N	<DEL>	sample001			dna	severus	PACBIO	PASS	60.0	True		100	60	60	120	0.5				ID=severus_DEL1;PRECISE=True;SVTYPE=DEL;SVLEN=100;END=7684393;STRANDS=+-;MAPQ=;GT=0/1;GQ=360;VAF=0.5;hVAF=1.00,0.00,0.00;DR=60;DV=60																				
+5	tumor_dna_severus_5_DEL_chr17:7685393_chr17:7685493	tumor	chr17	7685393	chr17	7685493	DEL	N	<DEL>	sample001			dna	severus	PACBIO	PASS	60.0	True		100	60	60	120	0.5				ID=severus_DEL2;PRECISE=True;SVTYPE=DEL;SVLEN=100;END=7685493;STRANDS=+-;MAPQ=;GT=0/1;GQ=360;VAF=0.5;hVAF=1.00,0.00,0.00;DR=60;DV=60																				

examples/run_vstol_vcf2tsv.sh

@@ -46,6 +46,25 @@ vstol vcf2tsv \
   --source-id hg002 \
   --output-tsv-file outputs/hg002_pbsv.tsv
 
+# savana
+vstol vcf2tsv \
+  --vcf-file ../test/data/sample001_savana_sv_breakpoints.vcf \
+  --variant-calling-method savana \
+  --sequencing-platform PACBIO \
+  --source-id sample001 \
+  --case-id tumor \
+  --control-id normal \
+  --output-tsv-file outputs/sample001_savana_sv_breakpoints.tsv
+
+# severus
+vstol vcf2tsv \
+  --vcf-file ../test/data/sample001_severus_somatic.vcf \
+  --variant-calling-method severus \
+  --sequencing-platform PACBIO \
+  --source-id sample001 \
+  --case-id tumor \
+  --output-tsv-file outputs/sample001_severus_somatic.tsv
+
 # sniffles2
 vstol vcf2tsv \
   --vcf-file ../test/data/hg002_sniffles2.vcf \
@@ -81,3 +100,13 @@ vstol vcf2tsv \
   --sequencing-platform PACBIO \
   --source-id hg002 \
   --output-tsv-file outputs/hg002_svim.tsv
+
+# svisionpro
+vstol vcf2tsv \
+  --vcf-file ../test/data/sample001.svision_pro_v1.8.s3.vcf \
+  --variant-calling-method svisionpro \
+  --sequencing-platform PACBIO \
+  --source-id sample001 \
+  --case-id tumor \
+  --control-id normal \
+  --output-tsv-file outputs/sample001.svision_pro_v1.8.s3.tsv

pyproject.toml

@@ -21,7 +21,7 @@ build-backend = "maturin"
 
 [project]
 name = "vstol"
-version = "0.2.2"
+version = "0.2.3"
 requires-python = ">=3.10"
 keywords = [
     "somatic variants",

python/vstolib/constants.py

@@ -95,9 +95,12 @@ class VariantCallingMethods:
     GATK4_MUTECT2 = 'gatk4-mutect2'
     LUMPY_SOMATIC = 'lumpy-somatic'
     PBSV = 'pbsv'
+    SAVANA = 'savana'
+    SEVERUS = 'severus'
     SNIFFLES2 = 'sniffles2'
     STRELKA2_SOMATIC = 'strelka2-somatic'
     SVIM = 'svim'
+    SVISIONPRO = 'svisionpro'
     ALL = [
         CUTESV,
         DBSNP,
@@ -106,9 +109,12 @@ class VariantCallingMethods:
         GATK4_MUTECT2,
         LUMPY_SOMATIC,
         PBSV,
+        SAVANA,
+        SEVERUS,
         SNIFFLES2,
         STRELKA2_SOMATIC,
-        SVIM
+        SVIM,
+        SVISIONPRO
     ]
 
     class AttributeTypes:
@@ -262,6 +268,54 @@ class AttributeTypes:
             'SAC': str,
             'NotFullySpanned': bool
         }
+        SAVANA = {
+            'ID': str,
+            'SVTYPE': str,
+            'MATEID': str,
+            'NORMAL_SUPPORT': int,
+            'TUMOUR_SUPPORT': int,
+            'SVLEN': int,
+            'BP_NOTATION': str,
+            'ORIGINATING_CLUSTER': str,
+            'END_CLUSTER': str,
+            'ORIGIN_STARTS_STD_DEV': float,
+            'ORIGIN_MAPQ_MEAN': float,
+            'ORIGIN_EVENT_SIZE_STD_DEV': float,
+            'ORIGIN_EVENT_SIZE_MEDIAN': float,
+            'ORIGIN_EVENT_SIZE_MEAN': float,
+            'END_STARTS_STD_DEV': float,
+            'END_MAPQ_MEAN': float,
+            'END_EVENT_SIZE_STD_DEV': float,
+            'END_EVENT_SIZE_MEDIAN': float,
+            'END_EVENT_SIZE_MEAN': float,
+            'TUMOUR_DP': str,
+            'NORMAL_DP': str,
+            'GT': str
+        }
+        SEVERUS = {
+            'ID': str,
+            'SVTYPE': str,
+            'SVLEN': int,
+            'CHR2': str,
+            'END': int,
+            'STRANDS': str,
+            'DETAILED_TYPE': str,
+            'INSLEN': int,
+            'MAPQ': int,
+            'PHASESETID': str,
+            'HP': int,
+            'CLUSTERID': str,
+            'INSSEQ': str,
+            'MATE_ID': str,
+            'INSIDE_VNTR': str,
+            'ALINGED_POS': str,
+            'GT': str,
+            'GQ': int,
+            'DR': int,
+            'DV': int,
+            'VAF': float,
+            'hVAF': str
+        }
         SNIFFLES2 = {
             'ID': str,
             'SVLEN': int,
@@ -368,6 +422,21 @@ class AttributeTypes:
             'AD': str,
             'CN': int
         }
+        SVISIONPRO = {
+            'ID': str,
+            'END': int,
+            'IT': str,
+            'SVLEN': int,
+            'BKPS': str,
+            'BKPSIT': str,
+            'SVTYPE': str,
+            'SUPPORT': int,
+            'VAF': float,
+            'RNAMES': str,
+            'GT': str,
+            'DR': int,
+            'DV': int
+        }
 
 
 class VariantCallTags:

python/vstolib/main.py

@@ -36,9 +36,12 @@
 from .vcf.gatk4_mutect2 import parse_gatk4_mutect2_callset
 from .vcf.lumpy import parse_lumpy_somatic_callset
 from .vcf.pbsv import parse_pbsv_callset
+from .vcf.savana import parse_savana_callset
+from .vcf.severus import parse_severus_callset
 from .vcf.sniffles2 import parse_sniffles2_callset
 from .vcf.strelka2 import parse_strelka2_somatic_callset
 from .vcf.svim import parse_svim_callset
+from .vcf.svisionpro import parse_svisionpro_callset
 
 
 logger = get_logger(__name__)
@@ -488,6 +491,21 @@ def vcf2tsv(
             sequencing_platform=sequencing_platform,
             source_id=source_id
         )
+    elif variant_calling_method == VariantCallingMethods.SAVANA:
+        variants_list = parse_savana_callset(
+            df_vcf=df_vcf,
+            sequencing_platform=sequencing_platform,
+            source_id=source_id,
+            case_id=case_id,
+            control_id=control_id
+        )
+    elif variant_calling_method == VariantCallingMethods.SEVERUS:
+        variants_list = parse_severus_callset(
+            df_vcf=df_vcf,
+            sequencing_platform=sequencing_platform,
+            source_id=source_id,
+            case_id=case_id
+        )
     elif variant_calling_method == VariantCallingMethods.SNIFFLES2:
         variants_list = parse_sniffles2_callset(
             df_vcf=df_vcf,
@@ -508,6 +526,14 @@ def vcf2tsv(
             sequencing_platform=sequencing_platform,
             source_id=source_id
         )
+    elif variant_calling_method == VariantCallingMethods.SVISIONPRO:
+        variants_list = parse_svisionpro_callset(
+            df_vcf=df_vcf,
+            sequencing_platform=sequencing_platform,
+            source_id=source_id,
+            case_id=case_id,
+            control_id=control_id
+        )
     elif variant_calling_method == VariantCallingMethods.DBSNP:
         variants_list = parse_dbsnp_callset(
             df_vcf=df_vcf,