diff --git a/annotate.nf b/annotate.nf
index eb2a420c8e..1d7f8bab8d 100644
--- a/annotate.nf
+++ b/annotate.nf
@@ -141,20 +141,21 @@ process RunSnpeff {
 
   output:
     set file("${vcf.baseName}.snpEff.ann.vcf"), file("${vcf.baseName}.snpEff.genes.txt"), file("${vcf.baseName}.snpEff.csv"), file("${vcf.baseName}.snpEff.summary.html") into snpeffReport
+		set variantCaller,file("${vcf.baseName}.snpEff.ann.vcf") into snpEffOutputVCFs
 
-  when: 'snpeff' in tools
+  when: 'snpeff' in tools || 'merge' in tools
 
   script:
   """
   java -Xmx${task.memory.toGiga()}g \
-  -jar \$SNPEFF_HOME/snpEff.jar \
-  ${snpeffDb} \
-  -csvStats ${vcf.baseName}.snpEff.csv \
-  -nodownload \
-  -cancer \
-  -v \
-  ${vcf} \
-  > ${vcf.baseName}.snpEff.ann.vcf
+	-jar \$SNPEFF_HOME/snpEff.jar \
+	${snpeffDb} \
+	-csvStats ${vcf.baseName}.snpEff.csv \
+	-nodownload \
+	-canon \
+	-v \
+	${vcf} \
+	> ${vcf.baseName}.snpEff.ann.vcf
 
   mv snpEff_summary.html ${vcf.baseName}.snpEff.summary.html
   """
@@ -165,6 +166,13 @@ if (params.verbose) snpeffReport = snpeffReport.view {
   File  : ${it.fileName}"
 }
 
+// When we are running in the 'merge' mode (first snpEff, then VEP)
+// we have to exchange the channels
+
+if('merge' in tools) {
+	vcfForVep = snpEffOutputVCFs
+}
+
 process RunVEP {
   tag {vcf}
 
@@ -176,7 +184,7 @@ process RunVEP {
   output:
     set file("${vcf.baseName}.vep.ann.vcf"), file("${vcf.baseName}.vep.summary.html") into vepReport
 
-  when: 'vep' in tools
+  when: 'vep' in tools || 'merge' in tools
 
   script:
   genome = params.genome == 'smallGRCh37' ? 'GRCh37' : params.genome
@@ -230,7 +238,8 @@ def defineDirectoryMap() {
 def defineToolList() {
   return [
     'snpeff',
-    'vep'
+    'vep',
+    'merge'
   ]
 }
 
@@ -252,6 +261,7 @@ def helpMessage() {
   log.info "       Possible values are:"
   log.info "         snpeff (use snpEff for Annotation of Variants)"
   log.info "         vep (use VEP for Annotation of Variants)"
+  log.info "         merge (first snpEff, then feed its output VCFs to VEP)"
   log.info "    --annotateTools"
   log.info "       Option to configure which tools to annotate."
   log.info "         Different tools to be separated by commas."
diff --git a/data/tumor_genes.bed b/data/tumor_genes.bed
index a54dd69b76..445f7ea463 100644
--- a/data/tumor_genes.bed
+++ b/data/tumor_genes.bed
@@ -4,6 +4,7 @@ chr1	3069168	3438621	PRDM16
 chr1	6181269	6209389	RPL22
 chr1	6785324	7769706	CAMTA1
 chr1	11106535	11262507	MTOR
+chr1	12644562	12667101	AADACL4
 chr1	13700198	13825079	PRDM2
 chr1	15847864	15940460	SPEN
 chr1	17018722	17054170	SDHB
@@ -12,7 +13,6 @@ chr1	19074506	19210276	UBR4
 chr1	23019448	23083689	KDM1A
 chr1	23557918	23559794	ID3
 chr1	23581495	23640568	MDS2
-chr1	26693236	26782104	ARID1A
 chr1	26949562	26960406	KDF1
 chr1	30931506	31065991	PUM1
 chr1	32251239	32286165	LCK
@@ -238,7 +238,6 @@ chr12	22625075	22690665	ETNK1
 chr12	25204789	25250936	KRAS
 chr12	27523431	27695564	PPFIBP1
 chr12	40196744	40369285	LRRK2
-chr12	45729665	45908040	ARID2
 chr12	47972965	48004486	COL2A1
 chr12	48328980	48330279	H1FNT
 chr12	49018975	49061895	KMT2D
@@ -338,7 +337,6 @@ chr14	99169287	99271524	BCL11B
 chr14	101964528	102050792	DYNC1H1
 chr14	102080738	102139699	HSP90AA1
 chr14	103100144	103110559	EXOC3L4
-chr14	104769349	104795751	AKT1
 chr14	104937244	104978357	AHNAK2
 chr14	105566277	106879844	IGH
 chr15	22184967	22185402	IGHV4OR15-8
@@ -596,7 +594,6 @@ chr2	21001429	21044073	APOB
 chr2	24029340	24049575	WDCP
 chr2	24491914	24770702	NCOA1
 chr2	25227855	25342590	DNMT3A
-chr2	25733753	25878516	ASXL2
 chr2	27537386	27582721	C2orf16
 chr2	29192774	29921566	ALK
 chr2	32357028	32618899	BIRC6
@@ -672,7 +669,6 @@ chr2	241734579	241768816	D2HGDH
 chr20	325595	330224	SOX12
 chr20	1894167	1940592	SIRPA
 chr20	20034368	20056046	CRNKL1
-chr20	32358344	32439319	ASXL1
 chr20	37344685	37406050	SRC
 chr20	40685848	40689240	MAFB
 chr20	41028818	41124487	TOP1
@@ -729,6 +725,7 @@ chr22	40410281	40636702	MKL1
 chr22	41091786	41180079	EP300
 chr22	46360834	46537170	CELSR1
 chr22	50674415	50733298	SHANK3
+chr3	132317373	132368327	ACPP	
 chr3	4493348	4847840	ITPR1
 chr3	8980591	9363053	SRGAP3
 chr3	9731729	9748018	BRPF1
@@ -997,7 +994,6 @@ chr7	137874979	138002067	CREB3L2
 chr7	138460334	138589993	TRIM24
 chr7	138831381	138981318	KIAA1549
 chr7	139230356	139308236	UBN2
-chr7	140719327	140924764	BRAF
 chr7	142111722	142223533	MGAM2
 chr7	142299011	142813287	TRB
 chr7	143353400	143362770	FAM131B
@@ -1141,7 +1137,6 @@ chrX	71144831	71171201	NLGN3
 chrX	71239624	71255146	ZMYM3
 chrX	71283192	71301168	NONO
 chrX	71366239	71532374	TAF1
-chrX	77504878	77786269	ATRX
 chrX	83861126	83886699	CYLC1
 chrX	100291644	100410273	PCDH19
 chrX	101349447	101390796	BTK
@@ -1165,3 +1160,307 @@ chrY	1187549	1212750	CRLF2
 chrY	1268800	1310381	CSF2RA
 chrY	1462572	1537107	P2RY8
 chrY	2691179	2741309	CD99
+chr1	1785285	1891117	GNB1
+chr1	6181269	6209389	RPL22
+chr1	8004404	8026308	ERRFI1
+chr1	9651732	9729114	PIK3CD
+chr1	16124337	16156087	EPHA2
+chr1	16740273	16972979	CROCC
+chr1	23691779	23696425	RPL11
+chr1	26693236	26782104	ARID1A
+chr1	27612064	27635277	FGR
+chr1	45012147	45015575	UROD
+chr1	47216290	47232220	TAL1
+chr1	48532855	50023913	AGBL4
+chr1	64833229	64966504	JAK1
+chr1	92832025	92841924	RPL5
+chr1	114704469	114716894	NRAS
+chr1	150574551	150579738	MCL1
+chr1	154405193	154469450	IL6R
+chr1	155897808	155911404	RIT1
+chr1	156463727	156500828	MEF2D
+chr1	218346235	218444619	TGFB2
+chr1	224114087	224162047	FBXO28
+chr1	241652278	241802133	WDR64
+chr1	245749342	246507312	SMYD3
+chr10	6427143	6580301	PRKCQ
+chr10	19048771	19790401	MALRD1
+chr10	21524675	21743630	MLLT10
+chr10	28532493	28623112	WAC
+chr10	52314296	52318042	DKK1
+chr10	79069035	79316528	ZMIZ1
+chr10	81875314	82987179	NRG3
+chr10	87863113	87971930	PTEN
+chr10	101130505	101137789	TLX1
+chr10	109996368	110135565	ADD3
+chr10	110567691	110604636	SMC3
+chr11	1995163	2001470	H19
+chr11	2608328	2699994	KCNQ1OT1
+chr11	2883213	2885881	CDKN1C
+chr11	3671083	3797792	NUP98
+chr11	9573681	9593457	WEE1
+chr11	32387775	32435630	WT1
+chr11	33858576	33892289	LMO2
+chr11	36510709	36593156	RAG1
+chr11	36575574	36598279	RAG2
+chr11	47354860	47378576	SPI1
+chr11	64234538	64238793	VEGFB
+chr11	69771016	69775403	FGF4
+chr11	69810224	69819024	FGF3
+chr11	70467856	71252577	SHANK2
+chr11	71428193	71452868	DHCR7
+chr11	86244544	86278813	EED
+chr11	118436490	118526832	KMT2A
+chr11	119084866	119093549	HMBS
+chr11	119206276	119313926	CBL
+chr11	125625136	125676255	CHEK1
+chr12	6570083	6607476	CHD4
+chr12	6666477	6689572	ZNF384
+chr12	11649854	11895402	ETV6
+chr12	12715058	12722371	CDKN1B
+chr12	14365632	14502935	ATF7IP
+chr12	25204789	25250936	KRAS
+chr12	45729665	45908040	ARID2
+chr12	47782722	47833132	HDAC7
+chr12	49018975	49059774	KMT2D
+chr12	51906908	51923361	ACVRL1
+chr12	55966769	55972784	CDK2
+chr12	65169571	65248327	LEMD3
+chr12	103930107	103953645	HSP90B1
+chr12	111405948	111451623	SH2B3
+chr12	112418351	112509913	PTPN11
+chr13	28003274	28100592	FLT3
+chr13	28300344	28495145	FLT1
+chr13	32586427	32778019	PDS5B
+chr13	40932028	41061440	ELF1
+chr13	44373665	44397714	SERP2
+chr13	48303751	48481986	RB1
+chr13	48389567	48444704	LPAR6
+chr13	50082171	50723236	DLEU1
+chr14	22422371	22423042	TRDV2
+chr14	22439007	22439015	TRDD2
+chr14	22449113	22449125	TRDD3
+chr14	22513939	22513998	TRAJ29
+chr14	34752731	34875647	BAZ1A
+chr14	45135940	45200890	FANCM
+chr14	56813183	57152177	OTX2-AS1
+chr14	60643415	60658259	SIX1
+chr14	61187559	61550976	PRKCH
+chr14	75958099	75982991	TGFB3
+chr14	94376747	94390693	SERPINA1
+chr14	103697609	103715504	XRCC3
+chr14	104769349	104795751	AKT1
+chr14	105864215	105864260	IGHJ4
+chr14	106775157	106775618	IGHV3-71
+chr15	34341713	34343177	NOP10
+chr15	40694774	40732339	RAD51
+chr15	40929340	40939072	DLL4
+chr15	40978880	41116354	INO80
+chr15	41557675	41583586	TYRO3
+chr15	41621224	41773081	MGA
+chr15	75935969	76059795	NRG4
+chr16	3581181	3611598	SLX4
+chr16	3651639	3717597	TRAP1
+chr16	3725054	3880726	CREBBP
+chr16	4257186	4273075	TFAP4
+chr16	4314761	4339597	GLIS2
+chr16	8892094	8964514	USP7
+chr16	15643267	15726353	NDE1
+chr16	23677656	23690367	PLK1
+chr16	30114105	30123506	MAPK3
+chr16	67029116	67101058	CBFB
+chr16	67562407	67639183	CTCF
+chr16	71637835	71724701	PHLPP2
+chr17	8204733	8210600	AURKB
+chr17	16029157	16218185	NCOR1
+chr17	20999593	21043760	USP22
+chr17	28950513	29057220	PIPOX
+chr17	31094927	31382116	NF1
+chr17	31937018	32001045	SUZ12
+chr17	39757715	39864188	IKZF3
+chr17	42199168	42276707	STAT5B
+chr17	58692573	58735611	RAD51C
+chr17	58982638	59106921	TRIM37
+chr17	59209400	59215247	SMG8
+chr17	59893046	59950564	RPS6KB1
+chr17	66302636	66810743	PRKCA
+chr17	72323123	72640472	LINC00511
+chr17	75318076	75405709	GRB2
+chr17	76470891	76501790	RHBDF2
+chr17	80544819	80966371	RPTOR
+chr17	81556887	81648465	NPLOC4
+chr18	12785478	12929643	PTPN2
+chr18	49041474	49461347	DYM
+chr18	62715450	62980433	PHLPP1
+chr19	851014	856247	ELANE
+chr19	1609290	1652605	TCF3
+chr19	4044364	4066945	ZBTB7A
+chr19	7112255	7294034	INSR
+chr19	10133345	10231286	DNMT1
+chr19	10718079	10833488	DNM2
+chr19	10961001	11065395	SMARCA4
+chr19	11377205	11384342	EPOR
+chr19	17824780	17848071	JAK3
+chr19	33299934	33302564	CEBPA
+chr19	34428352	34471251	UBA2
+chr19	39498895	39508481	DLL3
+chr19	41219203	41261766	AXL
+chr19	41301587	41353911	TGFB1
+chr19	45407333	45478828	ERCC1
+chr19	54137728	54155681	CNOT3
+chr19	54415219	54436900	TTYH1
+chr19	55654146	55674715	U2AF2
+chr19	57230802	57235548	AURKC
+chr2	15921037	15942249	MYCNOS
+chr2	15940564	15947007	MYCN
+chr2	16549459	16666331	FAM49A
+chr2	25733753	25878516	ASXL2
+chr2	43222402	43226609	ZFP36L2
+chr2	45005161	45009430	SIX2
+chr2	45651345	46187990	PRKCE
+chr2	47345158	47387601	EPCAM
+chr2	49918505	51225575	NRXN1
+chr2	58159243	58241372	FANCL
+chr2	73986404	74108176	TET3
+chr2	87755955	87825952	RGPD2
+chr2	111898479	112029561	MERTK
+chr2	112829751	112836903	IL1B
+chr2	144364364	144524583	ZEB2
+chr2	203867786	203873960	CTLA4
+chr2	212999691	213152427	IKZF2
+chr2	231961245	232344350	DIS3L2
+chr2	232697299	232860575	GIGYF2
+chr20	32052188	32101856	HCK
+chr20	32358344	32439319	ASXL1
+chr20	32762385	32809356	DNMT3B
+chr20	33273480	33309878	BPIFB1
+chr20	53567065	53609907	ZNF217
+chr20	56369389	56392337	AURKA
+chr20	61252426	61940617	CDH4
+chr21	34787801	36004667	RUNX1
+chr21	38380027	38661780	ERG
+chr21	38805307	38824955	ETS2
+chr22	20917426	20953749	CRKL
+chr22	22030934	22031472	IGLV4-69
+chr22	22887780	22896107	IGLL5
+chr22	28794555	28800597	XBP1
+chr22	30262829	30266840	OSM
+chr22	41091786	41180079	EP300
+chr22	50263713	50270767	MAPK11
+chr3	47016429	47163967	SETD2
+chr3	49887002	49903873	MST1R
+chr3	53156009	53192717	PRKCD
+chr3	66378797	66501263	LRIG1
+chr3	112332347	112362812	CD200
+chr3	116709235	116723581	TUSC7
+chr3	116716460	116716624	TUSC7
+chr3	128479427	128493185	GATA2
+chr3	164978898	165078495	SI
+chr3	177019340	177228000	TBL1XR1
+chr4	849276	932373	GAK
+chr4	24517441	24584550	DHX15
+chr4	39822863	39977956	PDS5A
+chr4	54657918	54740715	KIT
+chr4	105145875	105279816	TET2
+chr4	108047545	108168956	LEF1
+chr4	122826708	122898236	FGF2
+chr4	148078762	148444698	NR3C2
+chr4	152321259	152536101	FBXW7
+chr4	171812254	173041559	GALNTL6
+chr4	190173774	190185942	DUX4
+chr5	1225355	1246189	SLC6A18
+chr5	1253147	1295069	TERT
+chr5	31400497	31532196	DROSHA
+chr5	35852695	35879603	IL7R
+chr5	36876759	37066413	NIPBL
+chr5	38845858	38945596	OSMR
+chr5	68215720	68301821	PIK3R1
+chr5	69234795	69277430	CDK7
+chr5	87267888	87391931	RASA1
+chr5	88717117	88904257	MEF2C
+chr5	128257909	128659185	FBN2
+chr5	134114711	134151865	TCF7
+chr5	139846779	140043299	NRG2
+chr5	142592178	142698070	FGF1
+chr5	143277931	143435512	NR3C1
+chr5	158695916	159099761	EBF1
+chr5	171309284	171312134	TLX3
+chr5	171387116	171411137	NPM1
+chr5	178149460	178153967	NHP2
+chr6	1623806	2245692	GMDS
+chr6	10393186	10419659	TFAP2A
+chr6	19837386	19840684	ID4
+chr6	26087281	26098343	HFE
+chr6	29941260	29945884	HLA-A
+chr6	30876421	30900156	DDR1
+chr6	32194843	32224067	NOTCH4
+chr6	32517343	32530287	HLA-DRB5
+chr6	32578769	32589848	HLA-DRB1
+chr6	32628179	32647062	HLA-DQA1
+chr6	32659467	32668383	HLA-DQB1
+chr6	32756098	32763534	HLA-DQB2
+chr6	32968660	32981505	BRD2
+chr6	36027677	36111236	MAPK14
+chr6	41934933	42050357	CCND3
+chr6	43576150	43615660	POLH
+chr6	43770184	43786487	VEGFA
+chr6	63719980	65707225	EYS
+chr6	111660332	111873452	FYN
+chr6	135181315	135219173	MYB
+chr6	160991727	161117385	MAP3K4
+chr6	170282206	170306565	DLL1
+chr7	497258	520296	PDGFA
+chr7	5527151	5563784	ACTB
+chr7	18086949	19002416	HDAC9
+chr7	22725884	22732002	IL6
+chr7	27170591	27180261	HOXA10
+chr7	50304124	50405101	IKZF1
+chr7	69598919	70793068	AUTS2
+chr7	81699006	81770438	HGF
+chr7	100673531	100679174	GNB2
+chr7	105014179	105114361	KMT2E
+chr7	106865278	106907145	PIK3CG
+chr7	140719327	140924764	BRAF
+chr7	142749468	142753076	PRSS1
+chr7	148807383	148884321	EZH2
+chr7	151466012	151520120	RHEB
+chr7	155799986	155812273	SHH
+chr8	11494001	11564604	BLK
+chr8	11676959	11760002	GATA4
+chr8	55879813	56014168	LYN
+chr8	58805418	59119208	TOX
+chr8	97775057	97853013	LAPTM4B
+chr8	104590733	105804532	ZFPM2
+chr8	127735434	127741434	MYC
+chr8	140657900	141002216	PTK2
+chr9	4984390	5128183	JAK2
+chr9	8314246	10612723	PTPRD
+chr9	21802543	21937651	MTAP
+chr9	21967753	21995301	CDKN2A
+chr9	35657751	35658018	RMRP
+chr9	35657754	35658017	RMRP
+chr9	36833275	37034185	PAX5
+chr9	37120539	37358149	ZCCHC7
+chr9	127785679	127790787	CDK9
+chr9	127815012	127854756	ENG
+chr9	132592997	132670401	DDX31
+chr9	136494444	136545862	NOTCH1
+chrX	1187549	1212750	CRLF2
+chrX	41085635	41236579	USP9X
+chrX	44873177	45112602	KDM6A
+chrX	53082367	53088540	TSPYL2
+chrX	71118556	71142454	MED12
+chrX	74585217	74614617	RLIM
+chrX	77504878	77786269	ATRX
+chrX	107628424	107651026	PRPS1
+chrX	123960212	124422664	STAG2
+chrX	124227868	124373197	SH2D1A
+chrX	134373253	134428791	PHF6
+chrX	154389955	154409168	RPL10
+chrX	154762742	154777689	DKC1
+chrX	155997581	156010817	IL9R
+chrY	1187549	1212750	CRLF2
+chrY	2786855	2787699	SRY
+chrY	12701231	12860839	USP9Y
+chrY	13248379	13480673	UTY
+chrY	57184101	57197337	IL9R