Update/metafusion

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#117](https://github.com/mskcc/forte/pull/117) - add supporting-reads_gene-fusions\*.zip files to fusioncatcher outputs
 
 - [#118](https://github.com/mskcc/forte/pull/118) - change the way the plug-n-play starfusion reference is downloaded.
+- [#126](https://github.com/mskcc/forte/pull/126) - enable clinical genes prioritization in Metafusion
 
 - [#128](https://github.com/mskcc/forte/pull/128) - full support for GRCh38 added
 

assets/clinical_allowlist_hg19.txt

@@ -0,0 +1,319 @@
+gene_name	ensembl_transcript	refseq_transcript
+AR	ENST00000374690	NM_000044
+BTK	ENST00000308731	NM_000061
+CDKN2A	ENST00000304494	NM_000077
+EPOR	ENST00000222139	NM_000121
+ESR1	ENST00000206249	NM_000125
+FGFR2	ENST00000358487	NM_000141
+FGFR3	ENST00000440486	NM_000142
+JAK3	ENST00000458235	NM_000215
+KIT	ENST00000288135	NM_000222
+MET	ENST00000397752	NM_000245
+PTCH1	ENST00000331920	NM_000264
+NME1	ENST00000393196	NM_000269
+RAG1	ENST00000299440	NM_000448
+GNAS	ENST00000371085	NM_000516
+RAG2	ENST00000311485	NM_000536
+CD44	ENST00000428726	NM_000610
+CD79B	ENST00000006750	NM_000626
+BCL2	ENST00000333681	NM_000633
+CSF1	ENST00000329608	NM_000757
+DCK	ENST00000286648	NM_000788
+PGR	ENST00000325455	NM_000926
+RARA	ENST00000254066	NM_000964
+SS18	ENST00000415083	NM_001007559
+MYBL1	ENST00000522677	NM_001080416
+NUTM2A	ENST00000381707	NM_001099338
+BCOR	ENST00000378444	NM_001123385
+YAP1	ENST00000282441	NM_001130145
+MYB	ENST00000341911	NM_001130173
+BIRC3	ENST00000263464	NM_001165
+MEAF6	ENST00000296214	NM_001270875
+NUTM2B	ENST00000429828	NM_001278495
+EIF4A1	ENST00000293831	NM_001416
+ID4	ENST00000378700	NM_001546
+ACVR2A	ENST00000241416	NM_001616
+ARAF	ENST00000377045	NM_001654
+RHOA	ENST00000418115	NM_001664
+BCL6	ENST00000406870	NM_001706
+BMP7	ENST00000395863	NM_001719
+CCND2	ENST00000261254	NM_001759
+CCND3	ENST00000372991	NM_001760
+ENTPD1	ENST00000371205	NM_001776
+CDC25A	ENST00000302506	NM_001789
+CEBPE	ENST00000206513	NM_001805
+CEBPG	ENST00000284000	NM_001806
+ERBB3	ENST00000267101	NM_001982
+ETV6	ENST00000396373	NM_001987
+FOXO1	ENST00000379561	NM_002015
+FLT1	ENST00000282397	NM_002019
+GATA1	ENST00000376670	NM_002049
+IRF8	ENST00000268638	NM_002163
+IDH2	ENST00000330062	NM_002168
+IL7R	ENST00000303115	NM_002185
+ITPKB	ENST00000429204	NM_002221
+JAK1	ENST00000342505	NM_002227
+LMO1	ENST00000335790	NM_002315
+LTK	ENST00000263800	NM_002344
+MAL	ENST00000309988	NM_002371
+MN1	ENST00000302326	NM_002430
+IRF4	ENST00000380956	NM_002460
+MYH11	ENST00000300036	NM_002474
+NPM1	ENST00000296930	NM_002520
+NRAS	ENST00000369535	NM_002524
+NTRK1	ENST00000524377	NM_002529
+PBX1	ENST00000420696	NM_002585
+PDGFB	ENST00000331163	NM_002608
+PDGFRB	ENST00000261799	NM_002609
+PIM1	ENST00000373509	NM_002648
+PLAG1	ENST00000316981	NM_002655
+PPAT	ENST00000264220	NM_002703
+PRKACA	ENST00000308677	NM_002730
+PRKAR2B	ENST00000265717	NM_002736
+PRKCA	ENST00000413366	NM_002737
+PRKD1	ENST00000331968	NM_002742
+MAP2K1	ENST00000307102	NM_002755
+PTPN1	ENST00000371621	NM_002827
+PTPN11	ENST00000351677	NM_002834
+RAF1	ENST00000251849	NM_002880
+SOX11	ENST00000322002	NM_003108
+SRF	ENST00000265354	NM_003131
+STAT6	ENST00000300134	NM_003153
+TCF3	ENST00000262965	NM_003200
+TNFSF4	ENST00000281834	NM_003326
+TYK2	ENST00000525621	NM_003331
+XPO1	ENST00000401558	NM_003400
+HMGA2	ENST00000403681	NM_003483
+TP63	ENST00000264731	NM_003722
+RAB7L1	ENST00000367139	NM_003929
+NFKB1	ENST00000226574	NM_003998
+BCL2A1	ENST00000267953	NM_004049
+DNTT	ENST00000371174	NM_004088
+E2F2	ENST00000361729	NM_004091
+FLT3	ENST00000241453	NM_004119
+ALK	ENST00000389048	NM_004304
+BCR	ENST00000305877	NM_004327
+CALR	ENST00000316448	NM_004343
+CEBPA	ENST00000498907	NM_004364
+CREBBP	ENST00000262367	NM_004380
+ERBB2	ENST00000269571	NM_004448
+ETV5	ENST00000306376	NM_004454
+EZH2	ENST00000320356	NM_004456
+SH3BP5	ENST00000383791	NM_004844
+NRG2	ENST00000361474	NM_004883
+CDKN2B	ENST00000276925	NM_004936
+ETV1	ENST00000430479	NM_004956
+FUS	ENST00000254108	NM_004960
+JAK2	ENST00000381652	NM_004972
+KRAS	ENST00000311936	NM_004985
+PDCD1	ENST00000334409	NM_005018
+NUP214	ENST00000359428	NM_005085
+ABL1	ENST00000318560	NM_005157
+BCL3	ENST00000164227	NM_005178
+CBL	ENST00000264033	NM_005188
+CEBPD	ENST00000408965	NM_005195
+EGFR	ENST00000275493	NM_005228
+ERBB4	ENST00000342788	NM_005235
+EWSR1	ENST00000397938	NM_005243
+FGR	ENST00000374005	NM_005248
+FOS	ENST00000303562	NM_005252
+GLI1	ENST00000228682	NM_005269
+GRB7	ENST00000309156	NM_005310
+MPL	ENST00000372470	NM_005373
+SH2B3	ENST00000341259	NM_005475
+TLX1	ENST00000370196	NM_005521
+LMO2	ENST00000257818	NM_005574
+LYL1	ENST00000264824	NM_005583
+MUSK	ENST00000374448	NM_005592
+TMPRSS2	ENST00000332149	NM_005656
+PRKD3	ENST00000234179	NM_005813
+IDH1	ENST00000345146	NM_005896
+IKZF1	ENST00000331340	NM_006060
+TFG	ENST00000240851	NM_006070
+DNAJB1	ENST00000254322	NM_006145
+NFE2L2	ENST00000397062	NM_006164
+NTRK2	ENST00000277120	NM_006180
+PDGFRA	ENST00000257290	NM_006206
+PIK3CA	ENST00000263967	NM_006218
+TFE3	ENST00000315869	NM_006521
+NCOA2	ENST00000452400	NM_006540
+FOSB	ENST00000353609	NM_006732
+U2AF1	ENST00000291552	NM_006758
+YWHAE	ENST00000264335	NM_006761
+KAT6A	ENST00000265713	NM_006766
+PIM2	ENST00000376509	NM_006875
+DNMT3B	ENST00000328111	NM_006892
+PYCR1	ENST00000329875	NM_006907
+PICALM	ENST00000393346	NM_007166
+BRD3	ENST00000303407	NM_007371
+CHIC2	ENST00000263921	NM_012110
+MGEA5	ENST00000361464	NM_012215
+NFATC2	ENST00000371564	NM_012340
+RLF	ENST00000372771	NM_012421
+SF3B1	ENST00000335508	NM_012433
+STAT5B	ENST00000293328	NM_012448
+TNFRSF13B	ENST00000261652	NM_012452
+IKZF3	ENST00000346872	NM_012481
+FAM216A	ENST00000377673	NM_013300
+BLNK	ENST00000224337	NM_013314
+CD274	ENST00000381577	NM_014143
+SETD2	ENST00000409792	NM_014159
+LIMD1	ENST00000273317	NM_014240
+NEK6	ENST00000320246	NM_014397
+KIAA0101	ENST00000300035	NM_014736
+MAST1	ENST00000251472	NM_014975
+CAMTA1	ENST00000303635	NM_015215
+WWTR1	ENST00000360632	NM_015472
+VGLL3	ENST00000398399	NM_016206
+CYB5R2	ENST00000299498	NM_016229
+KLF2	ENST00000248071	NM_016270
+NUP98	ENST00000324932	NM_016320
+PAX5	ENST00000358127	NM_016734
+MBTD1	ENST00000586178	NM_017643
+EXOC2	ENST00000230449	NM_018303
+STRBP	ENST00000348403	NM_018387
+PAG1	ENST00000220597	NM_018440
+BATF3	ENST00000243440	NM_018664
+MAML3	ENST00000509479	NM_018717
+AICDA	ENST00000229335	NM_020661
+RET	ENST00000355710	NM_020975
+LZTS1	ENST00000381569	NM_021020
+TLX3	ENST00000296921	NM_021025
+RELA	ENST00000406246	NM_021975
+THADA	ENST00000405975	NM_022065
+PRDM16	ENST00000270722	NM_022114
+RBM15	ENST00000369784	NM_022768
+CBFB	ENST00000412916	NM_022845
+WHSC1L1	ENST00000317025	NM_023034
+FGFR1	ENST00000447712	NM_023110
+EBF1	ENST00000313708	NM_024007
+PHF1	ENST00000374516	NM_024165
+NOTCH2	ENST00000256646	NM_024408
+PDGFD	ENST00000393158	NM_025208
+PDCD1LG2	ENST00000397747	NM_025239
+ZCCHC7	ENST00000336755	NM_032226
+CARD11	ENST00000396946	NM_032415
+MAML2	ENST00000524717	NM_032427
+GLIS2	ENST00000433375	NM_032575
+GATA2	ENST00000341105	NM_032638
+RSPO3	ENST00000356698	NM_032784
+CCNB3	ENST00000376042	NM_033031
+CCND1	ENST00000227507	NM_053056
+BCL11B	ENST00000357195	NM_138576
+BAX	ENST00000345358	NM_138761
+TAF15	ENST00000605844	NM_139215
+HOXA9	ENST00000343483	NM_152739
+PTK2B	ENST00000346049	NM_173176
+JAZF1	ENST00000283928	NM_175061
+P2RY8	ENST00000381297	NM_178129
+RSPO2	ENST00000276659	NM_178565
+VGLL2	ENST00000326274	NM_182645
+PRKACB	ENST00000370685	NM_182948
+CREB3L2	ENST00000330387	NM_194071
+TERT	ENST00000310581	NM_198253
+SS18L1	ENST00000331758	NM_198935
+AKT1	ENST00000555528	NM_005163
+AR	ENST00000396043	NM_001011645
+ARHGAP26	ENST00000274498	NM_015071
+BCORL1	ENST00000540052	NM_021946
+BRAF	ENST00000288602	NM_004333
+BRD4	ENST00000263377	NM_058243
+CIC	ENST00000575354	NM_015125
+CSF1	ENST00000369802	NM_172212
+DEK	ENST00000397239	NM_003472
+EPC1	ENST00000263062	NM_025209
+ERG	ENST00000417133	NM_004449
+ESR1	ENST00000440973	NM_001122742
+ETV4	ENST00000319349	NM_001986
+FGF1	ENST00000378046	NM_00800
+FGFR1	ENST00000397091	NM_015850
+FGFR4	ENST00000292408	NM_002011
+GRM1	ENST00000492807	NM_001278065
+IGF1R	ENST00000268035	NM_000875
+LTK	ENST00000453182	NM_001135685
+MKL2	ENST00000574045	NM_014048
+NCOA1	ENST00000288599	NM_147223
+NCOA3	ENST00000372004	NM_006534
+NOTCH1	ENST00000277541	NM_017617
+NR4A3	ENST00000330847	NM_173200
+NRG1	ENST00000522402	NM_001159996
+NRG1	ENST00000341377	NM_004495
+NRG1	ENST00000356819	NM_013956
+NRG1	ENST00000287842	NM_013957
+NRG1	ENST00000520502	NM_013959
+NRG1	ENST00000520407	NM_013962
+NTRK1	ENST00000392302	NM_001007792
+NTRK3	ENST00000317501	NM_001007156
+NTRK3	ENST00000317501	NM_002530
+NUTM1	ENST00000333756	NM_175741
+PAX3	ENST00000392069	NM_181459
+PAX7	ENST00000375375	NM_002584
+PPARG	ENST00000287820	NM_015869
+PRB3	ENST00000381842	NM_006249
+PRKCB	ENST00000303531	NM_002738
+PRKD2	ENST00000433867	NM_016457
+RAD51B	ENST00000487270	NM_133509
+RET	ENST00000340058	NM_020630
+ROS1	ENST00000368508	NM_002944
+SS18	ENST00000269137	NM_005637
+STAT6	ENST00000300134	NM_001178078
+TCF12	ENST00000438423	NM_207036
+TFEB	ENST00000230323	NM_007162
+TMPRSS2	ENST00000398585	NM_001135099
+USP6	ENST00000574788	NM_004505
+AKT3	ENST00000366539	NM_005465
+ASXL1	ENST00000375687	NM_015338
+CCDC50	ENST00000392455	NM_174908
+CHD1	ENST00000284049	NM_001270
+CIITA	ENST00000324288	NM_000246
+CRLF2	ENST00000400841	NM_022148
+CSF1R	ENST00000286301	NM_005211
+CTLA4	ENST00000302823	NM_005214
+DLEU1	ENST00000378180	NR_002605
+FOXP1	ENST00000318789	NM_032682
+FUT8	ENST00000557164	NM_004480
+IL16	ENST00000394652	NM_004513
+KDM6A	ENST00000377967	NM_021140
+LRMP	ENST00000354454	NM_006152
+MALT1	ENST00000348428	NM_006785
+MECOM	ENST00000494292	NM_004991
+MKL1	ENST00000355630	NM_020831
+MLF1	ENST00000355893	NM_022443
+MLLT4	ENST00000392108	NM_001040000
+MUC1	ENST00000337604	NM_002456
+MYC	ENST00000377970	NM_002467
+MYD88	ENST00000396334	NM_002468
+NFKB2	ENST00000189444	NM_002502
+PLCG1	ENST00000244007	NM_002660
+PLCG2	ENST00000359376	NM_002661
+RANBP1	ENST00000331821	NM_002882
+RUNX1	ENST00000300305	NM_001754
+S1PR2	ENST00000590320	NM_004230
+SEMA6A	ENST00000343348	NM_020796
+SERPINA9	ENST00000337425	NM_175739
+SETBP1	ENST00000282030	NM_015559
+TAL1	ENST00000371884	NM_003189
+WT1	ENST00000332351	NM_000378
+ABL2	ENST00000512653	NM_005158
+ASB13	ENST00000479033	NR_0024581
+BMF	ENST00000354670	NM_033503
+CDK6	ENST00000265734	NM_001259
+CSF3R	ENST00000373103	NM_156039
+DENND3	ENST00000519811	NM_014957
+DNM2	ENST00000389253	NM_004945
+DNMT3A	ENST00000321117	NM_175629
+DUSP22	ENST00000344450	NM_020185
+FBXW7	ENST00000281708	NM_033632
+IKZF2	ENST00000457361	NM_016260
+KMT2A	ENST00000534358	NM_005933
+MLLT10	ENST00000377072	NM_004641
+MME	ENST00000460393	NM_000902
+NF1	ENST00000358273	NM_000267
+NT5C2	ENST00000343289	NM_012229
+PAICS	ENST00000264221	NM_006452
+PHF6	ENST00000370800	NM_032335
+PML	ENST00000395135	NM_002675
+SLC29A1	ENST00000427851	NM_001078175
+SRSF2	ENST00000359995	NM_003016
+STAT3	ENST00000404395	NM_003150
+STIL	ENST00000360380	NM_003035