updated example

Clinical-Genomics · Nov 19, 2021 · 258868e · 258868e
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diff --git a/docs/example/AKAP9_BRAF.html b/docs/example/AKAP9_BRAF.html
diff --git a/docs/example/BRD4-1_NUTM1.html b/docs/example/BRD4-1_NUTM1.html
diff --git a/docs/example/BRD4_NUTM1.html b/docs/example/BRD4_NUTM1.html
diff --git a/docs/example/CD74_AL132671.2.html b/docs/example/CD74_AL132671.2.html
diff --git a/docs/example/CD74_ROS1.html b/docs/example/CD74_ROS1.html
diff --git a/docs/example/CIC_DUX4.html b/docs/example/CIC_DUX4.html
diff --git a/docs/example/[email protected] b/docs/example/[email protected]
diff --git a/docs/example/EML4_ALK.html b/docs/example/EML4_ALK.html
diff --git a/docs/example/ETV6_NTRK3.html b/docs/example/ETV6_NTRK3.html
diff --git a/docs/example/EWSR1_ATF1.html b/docs/example/EWSR1_ATF1.html
diff --git a/docs/example/EWSR1_FLI1.html b/docs/example/EWSR1_FLI1.html
diff --git a/docs/example/FGFR3_TACC3.html b/docs/example/FGFR3_TACC3.html
diff --git a/docs/example/FIP1L1_PDGFRA.html b/docs/example/FIP1L1_PDGFRA.html
diff --git a/docs/example/GOPC_ROS1.html b/docs/example/GOPC_ROS1.html
diff --git a/docs/example/HOOK3_RET.html b/docs/example/HOOK3_RET.html
diff --git a/docs/example/IFT81_NDRG4.html b/docs/example/IFT81_NDRG4.html
diff --git a/docs/example/IGH@_CRLF2.html b/docs/example/IGH@_CRLF2.html
diff --git a/docs/example/[email protected] b/docs/example/[email protected]
diff --git a/docs/example/MT-ATP8_MT-ATP6.html b/docs/example/MT-ATP8_MT-ATP6.html
diff --git a/docs/example/NPM1_ALK.html b/docs/example/NPM1_ALK.html
diff --git a/docs/example/SLC6A15_MT-ND2.html b/docs/example/SLC6A15_MT-ND2.html
diff --git a/docs/example/TMPRSS2_ETV1.html b/docs/example/TMPRSS2_ETV1.html
diff --git a/docs/example/fusion_list.tsv b/docs/example/fusion_list.tsv
@@ -16,6 +16,7 @@ EML4--ALK
 MALT1--IGH@
 NPM1--ALK
 CD74--AL132671.2
+BRD4-1--NUTM1
 SLC6A15--MT-ND2
 MT-ATP8--MT-ATP6
 IFT81--NDRG4
diff --git a/docs/example/fusion_list_filtered.tsv b/docs/example/fusion_list_filtered.tsv
@@ -12,3 +12,4 @@ ETV6--NTRK3
 CIC--DUX4
 EML4--ALK
 NPM1--ALK
+BRD4-1--NUTM1
diff --git a/docs/example/fusions.json b/docs/example/fusions.json
@@ -0,0 +1 @@
+[{"Fusion":"FGFR3--TACC3","Databases":["FusionGDB","Mitelman","COSMIC"],"Score":1.0,"Explained score":"0.5 * (0.125 + 0.125 + 0.125 + 0.125 + 0.125 + 0.125 + 0.125 + 0.125) + 0.5 * (0.200 + 0.400 + 0.400)","ericscript":{"position":"4:1806934:+#4:1727977:+","discordant_reads":978,"junction_reads":378,"fusion_type":"Read-Through","gene_expr1":0.0,"gene_expr2":1.58,"gene_expr_fusion":101.36},"fusioncatcher":{"position":"4:1806934:+#4:1727977:+","common_mapping_reads":0,"spanning_pairs":820,"spanning_unique_reads":66,"longest_anchor":43,"fusion_type":"in-frame"},"starfusion":{"position":"4:1806934:+#4:1727977:+","junction_reads":261,"spanning_reads":637,"ffmp":71576.5981},"pizzly":{"pair_count":487,"split_count":231},"squid":{"position":"4:1806048-1806934:+#4:1727976-1728733:-","score":785},"dragen":{"position":"4:1806934:+#4:1727977:+","score":8},"arriba":{"position":"4:1806934#4:1727977","reading-frame":"out-of-frame","type":"duplication","split_reads1":"88","split_reads2":"97","discordant_mates":"300","coverage1":"245","coverage2":"418","confidence":"high"},"jaffa":{"position":"4:1806933:+#4:1727978:+","spanning_pairs":832,"spanning_reads":65,"inframe":"NA","aligns":"FALSE","rearrangement":"TRUE","classification":"LowConfidence","known":"Yes"}},{"Fusion":"GOPC--ROS1","Databases":["Mitelman","COSMIC"],"Score":0.65,"Explained score":"0.5 * (0.125 + 0.125 + 0.125 + 0.125) + 0.5 * (0.400 + 0.400)","ericscript":{"position":"6:117566854:-#6:117321394:-","discordant_reads":140,"junction_reads":73,"fusion_type":"intra-chromosomal","gene_expr1":0.0,"gene_expr2":2.11,"gene_expr_fusion":26.21},"fusioncatcher":{"position":"6:117566854:-#6:117321394:-","common_mapping_reads":0,"spanning_pairs":73,"spanning_unique_reads":22,"longest_anchor":30,"fusion_type":"in-frame"},"arriba":{"position":"6:117566854#6:117321394","reading-frame":"in-frame","type":"deletion/read-through","split_reads1":"35","split_reads2":"16","discordant_mates":"26","coverage1":"123","coverage2":"145","confidence":"high"},"jaffa":{"position":"6:117566854:-#6:117321394:-","spanning_pairs":65,"spanning_reads":11,"inframe":"TRUE","aligns":"TRUE","rearrangement":"FALSE","classification":"HighConfidence","known":"Yes"}},{"Fusion":"AKAP9--BRAF","Databases":["FusionGDB","Mitelman","COSMIC"],"Score":0.938,"Explained score":"0.5 * (0.125 + 0.125 + 0.125 + 0.125 + 0.125 + 0.125 + 0.125) + 0.5 * (0.200 + 0.400 + 0.400)","ericscript":{"position":"7:92003235:+#7:140787584:-","discordant_reads":11,"junction_reads":24,"fusion_type":"intra-chromosomal","gene_expr1":9.56,"gene_expr2":9.72,"gene_expr_fusion":37.9},"fusioncatcher":{"position":"7:92003235:+#7:140787584:-","common_mapping_reads":0,"spanning_pairs":10,"spanning_unique_reads":11,"longest_anchor":29,"fusion_type":"in-frame"},"starfusion":{"position":"7:92003235:+#7:140787584:-","junction_reads":6,"spanning_reads":4,"ffmp":797.0668},"pizzly":{"pair_count":4,"split_count":5},"squid":{"position":"7:92002951-92003235:+#7:140783020-140787584:+","score":8},"arriba":{"position":"7:92003235#7:140787584","reading-frame":"in-frame","type":"inversion","split_reads1":"2","split_reads2":"3","discordant_mates":"4","coverage1":"48","coverage2":"34","confidence":"high"},"jaffa":{"position":"7:92003235:+#7:140787584:-","spanning_pairs":7,"spanning_reads":8,"inframe":"TRUE","aligns":"TRUE","rearrangement":"TRUE","classification":"HighConfidence","known":"Yes"}},{"Fusion":"FIP1L1--PDGFRA","Databases":["FusionGDB","Mitelman"],"Score":0.488,"Explained score":"0.5 * (0.125 + 0.125 + 0.125) + 0.5 * (0.200 + 0.400)","ericscript":{"position":"4:53425965:+#4:54274925:+","discordant_reads":68,"junction_reads":39,"fusion_type":"intra-chromosomal","gene_expr1":0.0,"gene_expr2":0.01,"gene_expr_fusion":29.15},"fusioncatcher":{"position":"4:53425965:+#4:54274925:+","common_mapping_reads":0,"spanning_pairs":50,"spanning_unique_reads":42,"longest_anchor":45,"fusion_type":"in-frame"},"arriba":{"position":"4:53425965#4:54274925","reading-frame":"in-frame","type":"deletion","split_reads1":"31","split_reads2":"74","discordant_mates":"16","coverage1":"45","coverage2":"122","confidence":"high"}},{"Fusion":"BRD4--NUTM1","Databases":["FusionGDB","Mitelman"],"Score":0.738,"Explained score":"0.5 * (0.125 + 0.125 + 0.125 + 0.125 + 0.125 + 0.125 + 0.125) + 0.5 * (0.200 + 0.400)","ericscript":{"position":"19:15254152:-#15:34347969:+","discordant_reads":7,"junction_reads":13,"fusion_type":"inter-chromosomal","gene_expr1":4.19,"gene_expr2":17.98,"gene_expr_fusion":83.9},"fusioncatcher":{"position":"19:15254152:-#15:34347969:+","common_mapping_reads":0,"spanning_pairs":5,"spanning_unique_reads":9,"longest_anchor":30,"fusion_type":"in-frame"},"starfusion":{"position":"19:15254152:-#15:34347969:+","junction_reads":6,"spanning_reads":2,"ffmp":637.6535},"pizzly":{"pair_count":1,"split_count":6},"squid":{"position":"19:15254151-15254264:-#15:34347968-34348134:-","score":9},"arriba":{"position":"19:15254152#15:34347969","reading-frame":"in-frame","type":"translocation","split_reads1":"2","split_reads2":"5","discordant_mates":"1","coverage1":"101","coverage2":"10","confidence":"high"},"jaffa":{"position":"19:15254152:-#15:34347969:+","spanning_pairs":3,"spanning_reads":8,"inframe":"TRUE","aligns":"TRUE","rearrangement":"TRUE","classification":"HighConfidence","known":"Yes"}},{"Fusion":"HOOK3--RET","Databases":["FusionGDB","Mitelman","COSMIC"],"Score":0.875,"Explained score":"0.5 * (0.125 + 0.125 + 0.125 + 0.125 + 0.125 + 0.125) + 0.5 * (0.200 + 0.400 + 0.400)","ericscript":{"position":"8:42968214:+#10:43116584:+","discordant_reads":12,"junction_reads":21,"fusion_type":"inter-chromosomal","gene_expr1":2.44,"gene_expr2":3.31,"gene_expr_fusion":31.82},"fusioncatcher":{"position":"8:42968214:+#10:43116584:+","common_mapping_reads":0,"spanning_pairs":10,"spanning_unique_reads":10,"longest_anchor":29,"fusion_type":"in-frame"},"starfusion":{"position":"8:42968214:+#10:43116584:+","junction_reads":11,"spanning_reads":2,"ffmp":1036.1869},"pizzly":{"pair_count":2,"split_count":8},"squid":{"position":"8:42968010-42968214:+#10:43116583-43116731:-","score":11},"arriba":{"position":"8:42968214#10:43116584","reading-frame":"in-frame","type":"translocation","split_reads1":"9","split_reads2":"1","discordant_mates":"2","coverage1":"35","coverage2":"7","confidence":"high"}},{"Fusion":"TMPRSS2--ETV1","Databases":["FusionGDB","Mitelman","COSMIC"],"Score":0.875,"Explained score":"0.5 * (0.125 + 0.125 + 0.125 + 0.125 + 0.125 + 0.125) + 0.5 * (0.200 + 0.400 + 0.400)","ericscript":{"position":"21:41494380:-#7:13935843:-","discordant_reads":9,"junction_reads":16,"fusion_type":"inter-chromosomal","gene_expr1":0.0,"gene_expr2":17.69,"gene_expr_fusion":18.49},"fusioncatcher":{"position":"21:41494381:-#7:13935844:-","common_mapping_reads":0,"spanning_pairs":7,"spanning_unique_reads":10,"longest_anchor":38,"fusion_type":"in-frame"},"starfusion":{"position":"21:41494375:-#7:13935838:-","junction_reads":10,"spanning_reads":3,"ffmp":1036.1868},"squid":{"position":"7:13935707-13935838:+#21:41494374-41494578:-","score":12},"arriba":{"position":"21:41494375#7:13935838","reading-frame":"in-frame","type":"translocation","split_reads1":"3","split_reads2":"7","discordant_mates":"3","coverage1":"7","coverage2":"114","confidence":"medium"},"jaffa":{"position":"21:41494381:-#7:13935838:-","spanning_pairs":4,"spanning_reads":9,"inframe":"NA","aligns":"FALSE","rearrangement":"TRUE","classification":"LowConfidence","known":"Yes"}},{"Fusion":"CD74--ROS1","Databases":["FusionGDB","Mitelman","COSMIC"],"Score":0.875,"Explained score":"0.5 * (0.125 + 0.125 + 0.125 + 0.125 + 0.125 + 0.125) + 0.5 * (0.200 + 0.400 + 0.400)","ericscript":{"position":"5:150404680:-#6:117324415:-","discordant_reads":3,"junction_reads":14,"fusion_type":"inter-chromosomal","gene_expr1":2.44,"gene_expr2":2.11,"gene_expr_fusion":19.87},"fusioncatcher":{"position":"5:150404680:-#6:117324415:-","common_mapping_reads":0,"spanning_pairs":3,"spanning_unique_reads":7,"longest_anchor":30,"fusion_type":"in-frame"},"starfusion":{"position":"5:150404680:-#6:117324415:-","junction_reads":7,"spanning_reads":0,"ffmp":557.9468},"pizzly":{"pair_count":0,"split_count":2},"arriba":{"position":"5:150404680#6:117324415","reading-frame":"in-frame","type":"translocation","split_reads1":"2","split_reads2":"3","discordant_mates":"0","coverage1":"8","coverage2":"6","confidence":"high"},"jaffa":{"position":"5:150404680:-#6:117324415:-","spanning_pairs":1,"spanning_reads":2,"inframe":"TRUE","aligns":"TRUE","rearrangement":"TRUE","classification":"HighConfidence","known":"Yes"}},{"Fusion":"EWSR1--FLI1","Databases":["FusionGDB","Mitelman","COSMIC"],"Score":0.938,"Explained score":"0.5 * (0.125 + 0.125 + 0.125 + 0.125 + 0.125 + 0.125 + 0.125) + 0.5 * (0.200 + 0.400 + 0.400)","ericscript":{"position":"22:29287134:+#11:128807180:+","discordant_reads":9,"junction_reads":12,"fusion_type":"inter-chromosomal","gene_expr1":37.0,"gene_expr2":3.29,"gene_expr_fusion":600.14},"fusioncatcher":{"position":"22:29287134:+#11:128807180:+","common_mapping_reads":0,"spanning_pairs":9,"spanning_unique_reads":11,"longest_anchor":28,"fusion_type":"in-frame"},"starfusion":{"position":"22:29287134:+#11:128807180:+","junction_reads":4,"spanning_reads":3,"ffmp":557.9467},"pizzly":{"pair_count":2,"split_count":6},"dragen":{"position":"22:29287134:+#11:128807180:+","score":21},"arriba":{"position":"22:29287134#11:128807180","reading-frame":"in-frame","type":"translocation","split_reads1":"3","split_reads2":"3","discordant_mates":"3","coverage1":"1089","coverage2":"23","confidence":"medium"},"jaffa":{"position":"22:29287134:+#11:128807180:+","spanning_pairs":4,"spanning_reads":8,"inframe":"TRUE","aligns":"TRUE","rearrangement":"TRUE","classification":"HighConfidence","known":"Yes"}},{"Fusion":"EWSR1--ATF1","Databases":["FusionGDB","Mitelman","COSMIC"],"Score":0.938,"Explained score":"0.5 * (0.125 + 0.125 + 0.125 + 0.125 + 0.125 + 0.125 + 0.125) + 0.5 * (0.200 + 0.400 + 0.400)","ericscript":{"position":"22:29287134:+#12:50814280:+","discordant_reads":11,"junction_reads":25,"fusion_type":"inter-chromosomal","gene_expr1":37.0,"gene_expr2":12.27,"gene_expr_fusion":553.3},"fusioncatcher":{"position":"22:29287134:+#12:50814280:+","common_mapping_reads":0,"spanning_pairs":10,"spanning_unique_reads":10,"longest_anchor":30,"fusion_type":"in-frame"},"starfusion":{"position":"22:29287134:+#12:50814280:+","junction_reads":10,"spanning_reads":3,"ffmp":1036.1868},"pizzly":{"pair_count":3,"split_count":8},"squid":{"position":"22:29286921-29287134:+#12:50814279-50814439:-","score":10},"arriba":{"position":"22:29287134#12:50814280","reading-frame":"in-frame","type":"translocation","split_reads1":"5","split_reads2":"5","discordant_mates":"1","coverage1":"1089","coverage2":"142","confidence":"high"},"jaffa":{"position":"22:29287134:+#12:50814280:+","spanning_pairs":4,"spanning_reads":6,"inframe":"TRUE","aligns":"TRUE","rearrangement":"TRUE","classification":"HighConfidence","known":"Yes"}},{"Fusion":"ETV6--NTRK3","Databases":["FusionGDB","Mitelman","COSMIC"],"Score":0.938,"Explained score":"0.5 * (0.125 + 0.125 + 0.125 + 0.125 + 0.125 + 0.125 + 0.125) + 0.5 * (0.200 + 0.400 + 0.400)","ericscript":{"position":"12:11869970:+#15:87940752:-","discordant_reads":7,"junction_reads":24,"fusion_type":"inter-chromosomal","gene_expr1":9.48,"gene_expr2":0.45,"gene_expr_fusion":54.74},"fusioncatcher":{"position":"12:11869969:+#15:87940753:-","common_mapping_reads":0,"spanning_pairs":6,"spanning_unique_reads":8,"longest_anchor":29,"fusion_type":"in-frame"},"starfusion":{"position":"12:11869969:+#15:87940753:-","junction_reads":10,"spanning_reads":4,"ffmp":1115.8935},"pizzly":{"pair_count":2,"split_count":8},"squid":{"position":"12:11869684-11869969:+#15:87940621-87940753:+","score":10},"arriba":{"position":"12:11869969#15:87940753","reading-frame":"in-frame","type":"translocation","split_reads1":"5","split_reads2":"4","discordant_mates":"2","coverage1":"81","coverage2":"7","confidence":"high"},"jaffa":{"position":"12:11869969:+#15:87940753:-","spanning_pairs":6,"spanning_reads":6,"inframe":"TRUE","aligns":"TRUE","rearrangement":"TRUE","classification":"HighConfidence","known":"Yes"}},{"Fusion":"CIC--DUX4","Databases":["Mitelman","COSMIC"],"Score":0.525,"Explained score":"0.5 * (0.125 + 0.125) + 0.5 * (0.400 + 0.400)","ericscript":{"position":"19:42295048:+#4:190174447:+","discordant_reads":6,"junction_reads":6,"fusion_type":"inter-chromosomal","gene_expr1":0.0,"gene_expr2":1.34,"gene_expr_fusion":5.54},"fusioncatcher":{"position":"19:42295047:+#4:190174446:+","common_mapping_reads":0,"spanning_pairs":5,"spanning_unique_reads":5,"longest_anchor":34,"fusion_type":"in-frame"}},{"Fusion":"IGH@--CRLF2","Databases":[],"Score":0.062,"Explained score":"0.5 * (0.125) + 0.5 * ()","fusioncatcher":{"position":"14:105863258:+#X:105799296:-","common_mapping_reads":0,"spanning_pairs":32,"spanning_unique_reads":9,"longest_anchor":94,"fusion_type":"---/intergenic"}},{"Fusion":"DUX4--IGH@","Databases":[],"Score":0.062,"Explained score":"0.5 * (0.125) + 0.5 * ()","fusioncatcher":{"position":"4:190174997:+#14:190287409:+","common_mapping_reads":0,"spanning_pairs":5,"spanning_unique_reads":5,"longest_anchor":84,"fusion_type":"CDS(truncated)/---"}},{"Fusion":"EML4--ALK","Databases":["FusionGDB","Mitelman","COSMIC"],"Score":0.688,"Explained score":"0.5 * (0.125 + 0.125 + 0.125) + 0.5 * (0.200 + 0.400 + 0.400)","fusioncatcher":{"position":"2:42301391:+#2:29223587:-","common_mapping_reads":0,"spanning_pairs":4,"spanning_unique_reads":4,"longest_anchor":33,"fusion_type":"CDS(truncated)/UTR"},"starfusion":{"position":"2:42301394:+#2:29223584:-","junction_reads":4,"spanning_reads":4,"ffmp":637.6534},"arriba":{"position":"2:42301394#2:29223584","reading-frame":"in-frame","type":"inversion","split_reads1":"1","split_reads2":"3","discordant_mates":"3","coverage1":"71","coverage2":"7","confidence":"high"}},{"Fusion":"MALT1--IGH@","Databases":[],"Score":0.062,"Explained score":"0.5 * (0.125) + 0.5 * ()","fusioncatcher":{"position":"18:58669909:+#14:105888559:+","common_mapping_reads":0,"spanning_pairs":3,"spanning_unique_reads":3,"longest_anchor":34,"fusion_type":"intergenic/---"}},{"Fusion":"NPM1--ALK","Databases":["FusionGDB","Mitelman","COSMIC"],"Score":0.625,"Explained score":"0.5 * (0.125 + 0.125) + 0.5 * (0.200 + 0.400 + 0.400)","fusioncatcher":{"position":"5:171391799:+#2:29223528:-","common_mapping_reads":0,"spanning_pairs":3,"spanning_unique_reads":3,"longest_anchor":30,"fusion_type":"in-frame"},"starfusion":{"position":"5:171391799:+#2:29223528:-","junction_reads":1,"spanning_reads":2,"ffmp":239.1201}},{"Fusion":"CD74--AL132671.2","Databases":[],"Score":0.062,"Explained score":"0.5 * (0.125) + 0.5 * ()","starfusion":{"position":"5:150404680:-#6:117324415:-","junction_reads":3,"spanning_reads":0,"ffmp":239.12}},{"Fusion":"BRD4-1--NUTM1","Databases":[],"Score":0.125,"Explained score":"0.5 * (0.125 + 0.125) + 0.5 * ()","squid":{"position":"19:15254151-15254264:-#15:34347968-34348134:-","score":9},"arriba":{"position":"19:15254152#15:34347969","reading-frame":"in-frame","type":"translocation","split_reads1":"2","split_reads2":"5","discordant_mates":"1","coverage1":"101","coverage2":"10","confidence":"high"}},{"Fusion":"SLC6A15--MT-ND2","Databases":[],"Score":0.062,"Explained score":"0.5 * (0.125) + 0.5 * ()","dragen":{"position":"12:84883145:-#M:5264:+","score":65}},{"Fusion":"MT-ATP8--MT-ATP6","Databases":[],"Score":0.062,"Explained score":"0.5 * (0.125) + 0.5 * ()","dragen":{"position":"M:8427:+#M:8644:+","score":12}},{"Fusion":"IFT81--NDRG4","Databases":[],"Score":0.062,"Explained score":"0.5 * (0.125) + 0.5 * ()","dragen":{"position":"12:110167873:+#16:58512475:+","score":11}}]
diff --git a/docs/example/index.html b/docs/example/index.html
diff --git a/docs/usage.md b/docs/usage.md
@@ -13,6 +13,7 @@ fusion_report run "<SAMPLE NAME>" /path/to/output /path/to/db/ \
   --squid tests/test_data/squid.txt \
   --pizzly tests/test_data/pizzly.tsv \
   --dragen tests/test_data/dragen.tsv \
+  --jaffa tests/test_data/jaffa.csv \
   --allow-multiple-gene-symbols
 ```
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
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