From 4899d5e546bd43a637a247b4474268f8259c4b91 Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Thu, 31 Aug 2023 16:26:41 +0100
Subject: [PATCH] Update genome blacklists

---
 assets/blacklists/GCRh38-blacklist.bed | 1049 +++++++++++++++++++++++
 assets/blacklists/GRCh37-blacklist.bed |  822 +++++++++---------
 assets/blacklists/GRCm38-blacklist.bed |  723 ++++++++++++----
 assets/blacklists/GRCm39-blacklist.bed |  565 ++++++++++++
 assets/blacklists/hg38-blacklist.bed   | 1087 +++++++++++++++++++++++-
 assets/blacklists/mm10-blacklist.bed   |  723 ++++++++++++----
 assets/blacklists/mm39-blacklist.bed   |  565 ++++++++++++
 conf/igenomes.config                   |    2 +-
 8 files changed, 4758 insertions(+), 778 deletions(-)
 create mode 100644 assets/blacklists/GCRh38-blacklist.bed
 mode change 100755 => 100644 assets/blacklists/GRCm38-blacklist.bed
 create mode 100644 assets/blacklists/GRCm39-blacklist.bed
 mode change 100755 => 100644 assets/blacklists/mm10-blacklist.bed
 create mode 100644 assets/blacklists/mm39-blacklist.bed

diff --git a/assets/blacklists/GCRh38-blacklist.bed b/assets/blacklists/GCRh38-blacklist.bed
new file mode 100644
index 00000000..1e292c79
--- /dev/null
+++ b/assets/blacklists/GCRh38-blacklist.bed
@@ -0,0 +1,1049 @@
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diff --git a/assets/blacklists/GRCh37-blacklist.bed b/assets/blacklists/GRCh37-blacklist.bed
index dcf5caff..a33f3fff 100644
--- a/assets/blacklists/GRCh37-blacklist.bed
+++ b/assets/blacklists/GRCh37-blacklist.bed
@@ -1,411 +1,411 @@
-1	564449	570371	High_Mappability_island	1000	.     
-1	724136	727043	Satellite_repeat	1000	.     
-1	825006	825115	BSR/Beta	1000	.     
-1	2583334	2634374	Low_mappability_island	1000	.     
-1	4363064	4363242	(CATTC)n	1000	.     
-1	5725866	5736651	Low_mappability_island	1000	.     
-1	16839923	16841396	Low_mappability_island	1000	.     
-1	38077347	38077423	Low_mappability_island	1000	.     
-1	91852785	91853147	LSU-rRNA_Hsa	1000	.     
-1	104163724	104163860	Low_mappability_island	1000	.     
-1	108112972	108113707	LSU-rRNA_Hsa	1000	.     
-1	121351474	121487059	centromeric_repeat	1000	.     
-1	142535434	142543081	Satellite_repeat	1000	.     
-1	142723256	142723968	Low_mappability_island	1000	.     
-1	142792613	142793303	Low_mappability_island	1000	.     
-1	142835822	142837333	Low_mappability_island	1000	.     
-1	143274490	143284340	centromeric_repeat	1000	.     
-1	145277108	145277572	LSU-rRNA_Hsa	1000	.     
-1	149033183	149035829	Satellite_repeat	1000	.     
-1	156186169	156186712	High_Mappability_island	1000	.     
-1	224199390	224204260	Satellite_repeat	1000	.     
-1	233318467	233318516	(CATTC)n	1000	.     
-1	236260366	236260821	Low_mappability_island	1000	.     
-1	237766308	237766764	LSU-rRNA_Hsa	1000	.     
-1	238105345	238105511	Low_mappability_island	1000	.     
-1	238108025	238108378	Low_mappability_island	1000	.     
-1	238108645	238109697	Low_mappability_island	1000	.     
-10	18841533	18862467	(CATTC)n	1000	.     
-10	20035661	20037171	Low_mappability_island	1000	.     
-10	36722282	36723650	Low_mappability_island	1000	.     
-10	38772277	38819357	Satellite_repeat	1000	.     
-10	38868892	38889025	Satellite_repeat	1000	.     
-10	39076515	39155771	Satellite_repeat	1000	.     
-10	42354835	42548642	centromeric_repeat	1000	.     
-10	42596676	42602082	Satellite_repeat	1000	.     
-10	42596700	42602110	Satellite_repeat	1000	.     
-10	42661264	42667623	Satellite_repeat	1000	.     
-10	42790522	42818398	Satellite_repeat	1000	.     
-10	135498649	135502716	Satellite_repeat	1000	.     
-11	6831669	6831838	ALR/Alpha	1000	.     
-11	10529403	10531969	Low_mappability_island	1000	.     
-11	48671444	48902406	centromeric_repeat	1000	.     
-11	48931242	48964015	centromeric_repeat	1000	.     
-11	50318471	50784078	centromeric_repeat	1000	.     
-11	51090700	51374066	centromeric_repeat	1000	.     
-11	51567242	51594226	centromeric_repeat	1000	.     
-11	54694046	55027975	centromeric_repeat	1000	.     
-11	73221660	73221946	Low_mappability_island	1000	.     
-11	85194913	85195322	LSU-rRNA_Hsa	1000	.     
-11	87524468	87525005	Low_mappability_island	1000	.     
-11	103275584	103281729	Low_mappability_island	1000	.     
-11	122874287	122874443	Low_mappability_island	1000	.     
-12	20704285	20704583	SSU-rRNA_Hsa	1000	.     
-12	34372315	34372825	LSU-rRNA_Hsa	1000	.     
-12	34432130	34857010	centromeric_repeat	1000	.     
-12	37989447	38441828	centromeric_repeat	1000	.     
-12	38531376	38531930	LSU-rRNA_Hsa	1000	.     
-12	41757383	41757545	Low_mappability_island	1000	.     
-12	127650407	127651075	LSU-rRNA_Hsa	1000	.     
-12	132061320	132062046	Low_mappability_island	1000	.     
-13	56545728	56545925	Low_mappability_island	1000	.     
-13	110076444	110076782	Low_mappability_island	1000	.     
-14	18999935	19056900	centromeric_repeat	1000	.     
-14	32953263	32954381	Low_mappability_island	1000	.     
-14	84637832	84639038	Low_mappability_island	1000	.     
-14	90341302	90341516	SSU-rRNA_Hsa	1000	.     
-15	19999941	20044132	centromeric_repeat	1000	.     
-16	32493036	32570826	ALR/Alpha	1000	.     
-16	32590063	32598801	ALR/Alpha	1000	.     
-16	33237130	33241330	Low_mappability_island	1000	.     
-16	33864355	34023306	centromeric_repeat	1000	.     
-16	34180542	34197081	Satellite_repeat	1000	.     
-16	34530115	34542632	BSR/Beta	1000	.     
-16	35193580	35285885	centromeric_repeat	1000	.     
-16	46385718	46456668	Satellite_repeat	1000	.     
-16	46497639	46500515	Satellite_repeat	1000	.     
-16	47538629	47539297	LSU-rRNA_Hsa	1000	.     
-17	19355538	19356096	LSU-rRNA_Hsa	1000	.     
-17	19502495	19506773	Low_mappability_island	1000	.     
-17	21905167	21906712	centromeric_repeat	1000	.     
-17	22018524	22032049	Low_mappability_island	1000	.     
-17	22221073	22263006	centromeric_repeat	1000	.     
-17	25263010	25268059	Satellite_repeat	1000	.     
-17	25415551	25417559	telomeric_repeat	1000	.     
-17	31149365	31149981	High_Mappability_island	1000	.     
-17	33478114	33478372	LSU-rRNA_Hsa	1000	.     
-17	41381502	41382591	High_Mappability_island	1000	.     
-17	41463538	41464075	High_Mappability_island	1000	.     
-17	41464478	41465015	snRNA	1000	.     
-17	41465562	41467288	High_Mappability_island	1000	.     
-17	51183038	51183763	Low_mappability_island	1000	.     
-17	55868618	55868752	LSU-rRNA_Hsa	1000	.     
-17	75158031	75158430	LSU-rRNA_Hsa	1000	.     
-18	96416	97552	Satellite_repeat	1000	.     
-18	105658	112233	Satellite_repeat	1000	.     
-18	2842252	2842356	Low_mappability_island	1000	.     
-18	15393801	15393992	centromeric_repeat	1000	.     
-18	18510894	18520356	centromeric_repeat	1000	.     
-18	44126235	44126593	(CATTC)n	1000	.     
-18	45379603	45379864	Low_mappability_island	1000	.     
-18	50319086	50319301	Low_mappability_island	1000	.     
-18	77772846	77773065	LSU-rRNA_Hsa	1000	.     
-19	246006	247844	TAR1	1000	.     
-19	22877614	22877696	SSU-rRNA_Hsa	1000	.     
-19	23235030	23235504	BSR/Beta	1000	.     
-19	24182398	24186210	LSU-rRNA_Hsa	1000	.     
-19	24385474	24633168	centromeric_repeat	1000	.     
-19	27730611	28262682	centromeric_repeat	1000	.     
-19	36066445	36066810	LSU-rRNA_Hsa	1000	.     
-19	36756398	36800948	centromeric_repeat	1000	.     
-19	37759473	37797722	centromeric_repeat	1000	.     
-19	44914313	44916340	ACRO1	1000	.     
-19	44960681	44962681	ACRO1	1000	.     
-2	739925	740994	Low_mappability_island	1000	.     
-2	49456729	49457067	Low_mappability_island	1000	.     
-2	88124390	88124903	Low_mappability_island	1000	.     
-2	89830421	89880514	Satellite_repeat	1000	.     
-2	90371401	90394776	Satellite_repeat	1000	.     
-2	90443001	90545431	Low_mappability_island	1000	.     
-2	91595080	91616015	Satellite_repeat	1000	.     
-2	92267428	92326280	centromeric_repeat	1000	.     
-2	115695017	115695281	LSU-rRNA_Hsa	1000	.     
-2	117781085	117781300	Low_mappability_island	1000	.     
-2	132966248	132989300	centromeric_repeat	1000	.     
-2	132994855	133007983	ALR/Alpha	1000	.     
-2	133011824	133013298	SSU-rRNA_Hsa	1000	.     
-2	133036250	133040042	LSU-rRNA_Hsa	1000	.     
-2	133044095	133045945	ACRO1	1000	.     
-2	143848503	143848792	Low_mappability_island	1000	.     
-2	148022736	148022878	Low_mappability_island	1000	.     
-2	149639207	149639515	Low_mappability_island	1000	.     
-2	156120500	156120610	Low_mappability_island	1000	.     
-2	162135000	162139241	Low_mappability_island	1000	.     
-2	230045426	230045796	LSU-rRNA_Hsa	1000	.     
-20	26257032	26320267	centromeric_repeat	1000	.     
-20	29517710	29521147	centromeric_repeat	1000	.     
-20	29803876	29833334	centromeric_repeat	1000	.     
-20	55932703	55936114	chrM	1000	.     
-20	62916702	62918053	telomeric_repeat	1000	.     
-21	9647205	9648529	Low_mappability_island	1000	.     
-21	9694896	9704962	centromeric_repeat	1000	.     
-21	9825451	9827612	High_Mappability_island	1000	.     
-21	9827612	9845233	Low_mappability_island	1000	.     
-21	9881895	9882569	TAR1	1000	.     
-21	10084922	10088004	Satellite_repeat	1000	.     
-21	10492876	10493049	Low_mappability_island	1000	.     
-21	10599428	10599915	TAR1	1000	.     
-21	10697886	10860890	centromeric_repeat	1000	.     
-21	11186054	11188131	Satellite_repeat	1000	.     
-21	14338127	14369791	centromeric_repeat	1000	.     
-21	18800575	18800997	(GAGTG)n	1000	.     
-21	27228003	27228242	SSU-rRNA_Hsa	1000	.     
-21	46796081	46796336	Low_mappability_island	1000	.     
-22	16847814	16862659	Satellite_repeat	1000	.     
-22	18876789	18884510	Satellite_repeat	1000	.     
-3	25508897	25509131	Low_mappability_island	1000	.     
-3	73159606	73161131	snRNA	1000	.     
-3	75696297	75699304	BSR/Beta	1000	.     
-3	75717841	75720426	Satellite_repeat	1000	.     
-3	80995858	81014459	ALR/Alpha	1000	.     
-3	90311686	90507410	centromeric_repeat	1000	.     
-3	93504815	93519133	centromeric_repeat	1000	.     
-3	96335934	96337436	Low_mappability_island	1000	.     
-3	160665423	160665642	Low_mappability_island	1000	.     
-3	196625514	196625860	Satellite_repeat	1000	.     
-3	197825427	197834080	Low_mappability_island	1000	.     
-4	9987	12694	telomeric_repeat	1000	.     
-4	12276463	12292424	ALR/Alpha	1000	.     
-4	12641862	12642305	Low_mappability_island	1000	.     
-4	21583630	21583719	(GAATG)n	1000	.     
-4	27732004	27732240	Low_mappability_island	1000	.     
-4	47774268	47774416	Low_mappability_island	1000	.     
-4	49085372	49342114	centromeric_repeat	1000	.     
-4	49488472	49662085	centromeric_repeat	1000	.     
-4	52659961	52688986	centromeric_repeat	1000	.     
-4	56194229	56194584	Low_mappability_island	1000	.     
-4	65473858	65473941	Low_mappability_island	1000	.     
-4	68264186	68266830	centromeric_repeat	1000	.     
-4	70296565	70296841	LSU-rRNA_Hsa	1000	.     
-4	76807083	76807320	LSU-rRNA_Hsa	1000	.     
-4	78929660	78929920	Low_mappability_island	1000	.     
-4	156374749	156377226	chrM	1000	.     
-4	156384860	156387314	Low_mappability_island	1000	.     
-4	163342479	163342744	Low_mappability_island	1000	.     
-4	190190746	190203442	Low_mappability_island	1000	.     
-4	190801869	190802909	Low_mappability_island	1000	.     
-4	190943802	190943962	Satellite_repeat	1000	.     
-4	190987268	190990949	Satellite_repeat	1000	.     
-4	191026302	191044344	telomeric_repeat	1000	.     
-5	17517177	17600940	Low_mappability_island	1000	.     
-5	21477365	21497415	Low_mappability_island	1000	.     
-5	34177882	34197574	Low_mappability_island	1000	.     
-5	45908253	46411114	centromeric_repeat	1000	.     
-5	49405493	49554574	centromeric_repeat	1000	.     
-5	71146650	71146996	LSU-rRNA_Hsa	1000	.     
-5	79945807	79948223	Low_mappability_island	1000	.     
-5	93903068	93906726	Low_mappability_island	1000	.     
-5	97746525	97746679	Low_mappability_island	1000	.     
-5	99381556	99390873	Low_mappability_island	1000	.     
-5	105889063	105889263	chrM	1000	.     
-5	123095972	123097432	chrM	1000	.     
-5	134258949	134264271	Low_mappability_island	1000	.     
-5	174541634	174542177	SSU-rRNA_Hsa	1000	.     
-6	58735349	58739031	centromeric_repeat	1000	.     
-6	58745955	58780547	centromeric_repeat	1000	.     
-6	61880095	61944008	centromeric_repeat	1000	.     
-6	62189892	62206612	ALR/Alpha	1000	.     
-6	62207809	62230644	ALR/Alpha	1000	.     
-6	62283966	62284581	Low_mappability_island	1000	.     
-6	133593944	133594201	LSU-rRNA_Hsa	1000	.     
-6	137059142	137059326	SSU-rRNA_Hsa	1000	.     
-6	150665074	150665281	SSU-rRNA_Hsa	1000	.     
-6	157731310	157735525	Low_mappability_island	1000	.     
-7	43878355	43878530	TAR1	1000	.     
-7	45291517	45291740	Low_mappability_island	1000	.     
-7	56437808	56442977	Low_mappability_island	1000	.     
-7	57253980	57254183	Low_mappability_island	1000	.     
-7	57255310	57255444	Low_mappability_island	1000	.     
-7	57261829	57261998	Low_mappability_island	1000	.     
-7	57544726	57556913	Satellite_repeat	1000	.     
-7	57811488	57836990	centromeric_repeat	1000	.     
-7	57939184	58055539	centromeric_repeat	1000	.     
-7	61054285	62454680	centromeric_repeat	1000	.     
-7	64059157	64066183	BSR/Beta	1000	.     
-7	64951348	64956223	centromeric_repeat	1000	.     
-7	68201468	68201673	Low_mappability_island	1000	.     
-7	68527370	68527788	LSU-rRNA_Hsa	1000	.     
-7	80962907	80963147	SSU-rRNA_Hsa	1000	.     
-7	100550640	100551321	Low_mappability_island	1000	.     
-7	142372972	142375638	Low_mappability_island	1000	.     
-7	145694403	145694561	Low_mappability_island	1000	.     
-8	155512	157639	TAR1	1000	.     
-8	21455971	21456306	LSU-rRNA_Hsa	1000	.     
-8	32868966	32873279	Low_mappability_island	1000	.     
-8	43092737	43097573	Satellite_repeat	1000	.     
-8	43399486	43843604	centromeric_repeat	1000	.     
-8	46838215	47457541	centromeric_repeat	1000	.     
-8	47739043	47742797	Low_mappability_island	1000	.     
-8	47750844	47776101	BSR/Beta	1000	.     
-8	56754955	56755418	LSU-rRNA_Hsa	1000	.     
-8	69218401	69218922	LSU-rRNA_Hsa	1000	.     
-8	70602248	70602620	LSU-rRNA_Hsa	1000	.     
-8	77114154	77114389	Low_mappability_island	1000	.     
-8	100508010	100508287	Low_mappability_island	1000	.     
-9	10435	11574	TAR1	1000	.     
-9	4799734	4800000	SSU-rRNA_Hsa	1000	.     
-9	33656606	33659249	Low_mappability_island	1000	.     
-9	42819021	42832395	centromeric_repeat	1000	.     
-9	44070617	44070871	Low_mappability_island	1000	.     
-9	44873123	44902307	centromeric_repeat	1000	.     
-9	45355954	45357644	telomeric_repeat	1000	.     
-9	45435109	45443517	centromeric_repeat	1000	.     
-9	66494170	66494805	TAR1	1000	.     
-9	66767710	66864329	centromeric_repeat	1000	.     
-9	66970914	67005594	centromeric_repeat	1000	.     
-9	67315122	67321036	centromeric_repeat	1000	.     
-9	67789868	67792893	centromeric_repeat	1000	.     
-9	68410775	68435115	Low_mappability_island	1000	.     
-9	69677073	69687998	centromeric_repeat	1000	.     
-9	69689770	69711497	centromeric_repeat	1000	.     
-9	69947961	70011196	centromeric_repeat	1000	.     
-9	70076144	70076855	centromeric_repeat	1000	.     
-9	70318723	70327683	centromeric_repeat	1000	.     
-9	72653073	72653572	Satellite_repeat	1000	.     
-9	78790077	78790255	(GAATG)n	1000	.     
-9	79186574	79187026	LSU-rRNA_Hsa	1000	.     
-9	141019938	141021783	TAR1	1000	.     
-MT	1	16569	chrM	1000	.     
-X	55206111	55206740	Low_mappability_island	1000	.     
-X	55207753	55208152	Low_mappability_island	1000	.     
-X	55208300	55208643	Low_mappability_island	1000	.     
-X	55208980	55209208	Low_mappability_island	1000	.     
-X	55209655	55210006	Low_mappability_island	1000	.     
-X	58330488	58330843	centromeric_repeat	1000	.     
-X	58373806	58373962	centromeric_repeat	1000	.     
-X	58377680	58377864	centromeric_repeat	1000	.     
-X	58415350	58416387	centromeric_repeat	1000	.     
-X	58432411	58432680	centromeric_repeat	1000	.     
-X	58485887	58486241	centromeric_repeat	1000	.     
-X	58488898	58494528	centromeric_repeat	1000	.     
-X	58499466	58504235	centromeric_repeat	1000	.     
-X	58506076	58528214	centromeric_repeat	1000	.     
-X	58528184	58536883	centromeric_repeat	1000	.     
-X	58544061	58582415	centromeric_repeat	1000	.     
-X	61681834	61919683	centromeric_repeat	1000	.     
-X	62003205	62041580	centromeric_repeat	1000	.     
-X	83658929	83659019	Low_mappability_island	1000	.     
-X	108297348	108297886	LSU-rRNA_Hsa	1000	.     
-X	114959057	115006437	Low_mappability_island	1000	.     
-X	125605623	125607351	Low_mappability_island	1000	.     
-X	125714985	125715338	Low_mappability_island	1000	.     
-X	125864844	125864980	Low_mappability_island	1000	.     
-X	125865719	125865874	Low_mappability_island	1000	.     
-Y	313470	313613	ALR/Alpha	1000	.     
-Y	3004989	3005175	LSU-rRNA_Hsa	1000	.     
-Y	4212807	4212910	Low_mappability_island	1000	.     
-Y	7671817	7694928	BSR/Beta	1000	.     
-Y	7726064	7730229	BSR/Beta	1000	.     
-Y	7730734	7731598	BSR/Beta	1000	.     
-Y	7735811	7752887	BSR/Beta	1000	.     
-Y	7785067	7806311	BSR/Beta	1000	.     
-Y	7806856	7814704	BSR/Beta	1000	.     
-Y	7815230	7820478	BSR/Beta	1000	.     
-Y	7829937	7832032	BSR/Beta	1000	.     
-Y	7832744	7848695	BSR/Beta	1000	.     
-Y	7870343	7873582	BSR/Beta	1000	.     
-Y	7874115	7874584	BSR/Beta	1000	.     
-Y	7875409	7885257	BSR/Beta	1000	.     
-Y	7886545	7894591	BSR/Beta	1000	.     
-Y	7898927	7916812	BSR/Beta	1000	.     
-Y	7918790	7921352	BSR/Beta	1000	.     
-Y	7926344	7936705	BSR/Beta	1000	.     
-Y	7941130	7947438	BSR/Beta	1000	.     
-Y	7948790	7964448	BSR/Beta	1000	.     
-Y	8179010	8181143	BSR/Beta	1000	.     
-Y	8181757	8213330	BSR/Beta	1000	.     
-Y	8214629	8215637	BSR/Beta	1000	.     
-Y	8220421	8230061	BSR/Beta	1000	.     
-Y	8230686	8231546	BSR/Beta	1000	.     
-Y	8240772	8265916	BSR/Beta	1000	.     
-Y	8291535	8292942	BSR/Beta	1000	.     
-Y	8294002	8295175	BSR/Beta	1000	.     
-Y	8296944	8321375	BSR/Beta	1000	.     
-Y	8325813	8325929	BSR/Beta	1000	.     
-Y	8326678	8333466	BSR/Beta	1000	.     
-Y	8334027	8342387	BSR/Beta	1000	.     
-Y	8356544	8369346	BSR/Beta	1000	.     
-Y	8909560	8909925	TAR1	1000	.     
-Y	8979478	8979585	Low_mappability_island	1000	.     
-Y	9072781	9072993	TAR1	1000	.     
-Y	9908430	9925608	centromeric_repeat	1000	.     
-Y	9981952	9982126	BSR/Beta	1000	.     
-Y	10034864	10036712	SSU-rRNA_Hsa	1000	.     
-Y	10040627	10045657	ALR/Alpha	1000	.     
-Y	10047773	10052533	ALR/Alpha	1000	.     
-Y	10053695	10057722	ALR/Alpha	1000	.     
-Y	10059394	10073694	ALR/Alpha	1000	.     
-Y	10075082	10075781	ALR/Alpha	1000	.     
-Y	10080736	10104539	ALR/Alpha	1000	.     
-Y	13104530	13144368	centromeric_repeat	1000	.     
-Y	13193966	13196535	Low_mappability_island	1000	.     
-Y	13252193	13259484	centromeric_repeat	1000	.     
-Y	13290177	13290667	chrM	1000	.     
-Y	13445957	13490591	Satellite_repeat	1000	.     
-Y	13642186	13749784	Satellite_repeat	1000	.     
-Y	13798522	13870984	Satellite_repeat	1000	.     
-Y	19691913	19692524	LSU-rRNA_Hsa	1000	.     
-Y	19764063	19776198	ALR/Alpha	1000	.     
-Y	19780600	19781704	ALR/Alpha	1000	.     
-Y	19783669	19796396	ALR/Alpha	1000	.     
-Y	19800068	19801419	ALR/Alpha	1000	.     
-Y	19808085	19817100	ALR/Alpha	1000	.     
-Y	19944298	19944581	TAR1	1000	.     
-Y	20235195	20235478	TAR1	1000	.     
-Y	20362679	20371694	ALR/Alpha	1000	.     
-Y	20378360	20379711	ALR/Alpha	1000	.     
-Y	20383383	20396110	ALR/Alpha	1000	.     
-Y	20398075	20399179	ALR/Alpha	1000	.     
-Y	20403581	20415713	ALR/Alpha	1000	.     
-Y	20487248	20487859	LSU-rRNA_Hsa	1000	.     
-Y	23124788	23125577	BSR/Beta	1000	.     
-Y	23149027	23151205	BSR/Beta	1000	.     
-Y	23157969	23158245	BSR/Beta	1000	.     
-Y	23159001	23167737	BSR/Beta	1000	.     
-Y	23178886	23181770	BSR/Beta	1000	.     
-Y	23220740	23223625	BSR/Beta	1000	.     
-Y	23234125	23235822	BSR/Beta	1000	.     
-Y	23236898	23248080	BSR/Beta	1000	.     
-Y	23248729	23248851	BSR/Beta	1000	.     
-Y	23899295	23899388	TAR1	1000	.     
-Y	23956449	23956628	TAR1	1000	.     
-Y	24247659	24247700	TAR1	1000	.     
-Y	24630999	24631040	TAR1	1000	.     
-Y	24953159	24975657	BSR/Beta	1000	.     
-Y	24980997	24991235	BSR/Beta	1000	.     
-Y	25022753	25039185	BSR/Beta	1000	.     
-Y	25040153	25042421	BSR/Beta	1000	.     
-Y	25048332	25059258	BSR/Beta	1000	.     
-Y	25060235	25064798	BSR/Beta	1000	.     
-Y	25099139	25121882	BSR/Beta	1000	.     
-Y	25122419	25160800	BSR/Beta	1000	.     
-Y	25182404	25192372	BSR/Beta	1000	.     
-Y	25217722	25219409	BSR/Beta	1000	.     
-Y	25493588	25495275	BSR/Beta	1000	.     
-Y	26148315	26148450	TAR1	1000	.     
-Y	26586905	26609405	BSR/Beta	1000	.     
-Y	26614745	26624983	BSR/Beta	1000	.     
-Y	26656502	26672934	BSR/Beta	1000	.     
-Y	26673902	26676170	BSR/Beta	1000	.     
-Y	26682081	26693007	BSR/Beta	1000	.     
-Y	26693984	26698547	BSR/Beta	1000	.     
-Y	26732883	26755623	BSR/Beta	1000	.     
-Y	26756160	26794538	BSR/Beta	1000	.     
-Y	26816148	26826116	BSR/Beta	1000	.     
-Y	26851466	26853153	BSR/Beta	1000	.     
-Y	27109247	27110934	BSR/Beta	1000	.     
-Y	27136281	27146249	BSR/Beta	1000	.     
-Y	27167859	27206241	BSR/Beta	1000	.     
-Y	27206778	27229502	BSR/Beta	1000	.     
-Y	27263848	27268411	BSR/Beta	1000	.     
-Y	27269388	27280315	BSR/Beta	1000	.     
-Y	27286226	27288494	BSR/Beta	1000	.     
-Y	27289462	27305895	BSR/Beta	1000	.     
-Y	27337415	27347656	BSR/Beta	1000	.     
-Y	27352996	27375497	BSR/Beta	1000	.     
-Y	27813984	27814119	TAR1	1000	.     
-Y	28555026	28555353	TAR1	1000	.     
-Y	28784129	28819695	Satellite_repeat	1000	.     
-Y	58819367	58917648	(CATTC)n	1000	.     
-Y	58971913	58997782	(CATTC)n	1000	.     
-Y	59361267	59362785	TAR1	1000	.     
\ No newline at end of file
+chr1	564450	570372
+chr1	724137	727044
+chr1	825007	825116
+chr1	2583335	2634375
+chr1	4363065	4363243
+chr1	5725867	5736652
+chr1	16839924	16841397
+chr1	38077348	38077424
+chr1	91852786	91853148
+chr1	104163725	104163861
+chr1	108112973	108113708
+chr1	121351475	121487060
+chr1	142535435	142543082
+chr1	142723257	142723969
+chr1	142792614	142793304
+chr1	142835823	142837334
+chr1	143274491	143284341
+chr1	145277109	145277573
+chr1	149033184	149035830
+chr1	156186170	156186713
+chr1	224199391	224204261
+chr1	233318468	233318517
+chr1	236260367	236260822
+chr1	237766309	237766765
+chr1	238105346	238105512
+chr1	238108026	238108379
+chr1	238108646	238109698
+chr10	18841534	18862468
+chr10	20035662	20037172
+chr10	36722283	36723651
+chr10	38772278	38819358
+chr10	38868893	38889026
+chr10	39076516	39155772
+chr10	42354836	42548643
+chr10	42596677	42602083
+chr10	42596701	42602111
+chr10	42661265	42667624
+chr10	42790523	42818399
+chr10	135498650	135502717
+chr11	6831670	6831839
+chr11	10529404	10531970
+chr11	48671445	48902407
+chr11	48931243	48964016
+chr11	50318472	50784079
+chr11	51090701	51374067
+chr11	51567243	51594227
+chr11	54694047	55027976
+chr11	73221661	73221947
+chr11	85194914	85195323
+chr11	87524469	87525006
+chr11	103275585	103281730
+chr11	122874288	122874444
+chr12	20704286	20704584
+chr12	34372316	34372826
+chr12	34432131	34857011
+chr12	37989448	38441829
+chr12	38531377	38531931
+chr12	41757384	41757546
+chr12	127650408	127651076
+chr12	132061321	132062047
+chr13	56545729	56545926
+chr13	110076445	110076783
+chr14	18999936	19056901
+chr14	32953264	32954382
+chr14	84637833	84639039
+chr14	90341303	90341517
+chr15	19999942	20044133
+chr16	32493037	32570827
+chr16	32590064	32598802
+chr16	33237131	33241331
+chr16	33864356	34023307
+chr16	34180543	34197082
+chr16	34530116	34542633
+chr16	35193581	35285886
+chr16	46385719	46456669
+chr16	46497640	46500516
+chr16	47538630	47539298
+chr17	19355539	19356097
+chr17	19502496	19506774
+chr17	21905168	21906713
+chr17	22018525	22032050
+chr17	22221074	22263007
+chr17	25263011	25268060
+chr17	25415552	25417560
+chr17	31149366	31149982
+chr17	33478115	33478373
+chr17	41381503	41382592
+chr17	41463539	41464076
+chr17	41464479	41465016
+chr17	41465563	41467289
+chr17	51183039	51183764
+chr17	55868619	55868753
+chr17	75158032	75158431
+chr18	96417	97553
+chr18	105659	112234
+chr18	2842253	2842357
+chr18	15393802	15393993
+chr18	18510895	18520357
+chr18	44126236	44126594
+chr18	45379604	45379865
+chr18	50319087	50319302
+chr18	77772847	77773066
+chr19	246007	247845
+chr19	22877615	22877697
+chr19	23235031	23235505
+chr19	24182399	24186211
+chr19	24385475	24633169
+chr19	27730612	28262683
+chr19	36066446	36066811
+chr19	36756399	36800949
+chr19	37759474	37797723
+chr19	44914314	44916341
+chr19	44960682	44962682
+chr2	739926	740995
+chr2	49456730	49457068
+chr2	88124391	88124904
+chr2	89830422	89880515
+chr2	90371402	90394777
+chr2	90443002	90545432
+chr2	91595081	91616016
+chr2	92267429	92326281
+chr2	115695018	115695282
+chr2	117781086	117781301
+chr2	132966249	132989301
+chr2	132994856	133007984
+chr2	133011825	133013299
+chr2	133036251	133040043
+chr2	133044096	133045946
+chr2	143848504	143848793
+chr2	148022737	148022879
+chr2	149639208	149639516
+chr2	156120501	156120611
+chr2	162135001	162139242
+chr2	230045427	230045797
+chr20	26257033	26320268
+chr20	29517711	29521148
+chr20	29803877	29833335
+chr20	55932704	55936115
+chr20	62916703	62918054
+chr21	9647206	9648530
+chr21	9694897	9704963
+chr21	9825452	9827613
+chr21	9827613	9845234
+chr21	9881896	9882570
+chr21	10084923	10088005
+chr21	10492877	10493050
+chr21	10599429	10599916
+chr21	10697887	10860891
+chr21	11186055	11188132
+chr21	14338128	14369792
+chr21	18800576	18800998
+chr21	27228004	27228243
+chr21	46796082	46796337
+chr22	16847815	16862660
+chr22	18876790	18884511
+chr3	25508898	25509132
+chr3	73159607	73161132
+chr3	75696298	75699305
+chr3	75717842	75720427
+chr3	80995859	81014460
+chr3	90311687	90507411
+chr3	93504816	93519134
+chr3	96335935	96337437
+chr3	160665424	160665643
+chr3	196625515	196625861
+chr3	197825428	197834081
+chr4	9988	12695
+chr4	12276464	12292425
+chr4	12641863	12642306
+chr4	21583631	21583720
+chr4	27732005	27732241
+chr4	47774269	47774417
+chr4	49085373	49342115
+chr4	49488473	49662086
+chr4	52659962	52688987
+chr4	56194230	56194585
+chr4	65473859	65473942
+chr4	68264187	68266831
+chr4	70296566	70296842
+chr4	76807084	76807321
+chr4	78929661	78929921
+chr4	156374750	156377227
+chr4	156384861	156387315
+chr4	163342480	163342745
+chr4	190190747	190203443
+chr4	190801870	190802910
+chr4	190943803	190943963
+chr4	190987269	190990950
+chr4	191026303	191044345
+chr5	17517178	17600941
+chr5	21477366	21497416
+chr5	34177883	34197575
+chr5	45908254	46411115
+chr5	49405494	49554575
+chr5	71146651	71146997
+chr5	79945808	79948224
+chr5	93903069	93906727
+chr5	97746526	97746680
+chr5	99381557	99390874
+chr5	105889064	105889264
+chr5	123095973	123097433
+chr5	134258950	134264272
+chr5	174541635	174542178
+chr6	58735350	58739032
+chr6	58745956	58780548
+chr6	61880096	61944009
+chr6	62189893	62206613
+chr6	62207810	62230645
+chr6	62283967	62284582
+chr6	133593945	133594202
+chr6	137059143	137059327
+chr6	150665075	150665282
+chr6	157731311	157735526
+chr7	43878356	43878531
+chr7	45291518	45291741
+chr7	56437809	56442978
+chr7	57253981	57254184
+chr7	57255311	57255445
+chr7	57261830	57261999
+chr7	57544727	57556914
+chr7	57811489	57836991
+chr7	57939185	58055540
+chr7	61054286	62454681
+chr7	64059158	64066184
+chr7	64951349	64956224
+chr7	68201469	68201674
+chr7	68527371	68527789
+chr7	80962908	80963148
+chr7	100550641	100551322
+chr7	142372973	142375639
+chr7	145694404	145694562
+chr8	155513	157640
+chr8	21455972	21456307
+chr8	32868967	32873280
+chr8	43092738	43097574
+chr8	43399487	43843605
+chr8	46838216	47457542
+chr8	47739044	47742798
+chr8	47750845	47776102
+chr8	56754956	56755419
+chr8	69218402	69218923
+chr8	70602249	70602621
+chr8	77114155	77114390
+chr8	100508011	100508288
+chr9	10436	11575
+chr9	4799735	4800001
+chr9	33656607	33659250
+chr9	42819022	42832396
+chr9	44070618	44070872
+chr9	44873124	44902308
+chr9	45355955	45357645
+chr9	45435110	45443518
+chr9	66494171	66494806
+chr9	66767711	66864330
+chr9	66970915	67005595
+chr9	67315123	67321037
+chr9	67789869	67792894
+chr9	68410776	68435116
+chr9	69677074	69687999
+chr9	69689771	69711498
+chr9	69947962	70011197
+chr9	70076145	70076856
+chr9	70318724	70327684
+chr9	72653074	72653573
+chr9	78790078	78790256
+chr9	79186575	79187027
+chr9	141019939	141021784
+chrM	2	16572
+chrX	55206112	55206741
+chrX	55207754	55208153
+chrX	55208301	55208644
+chrX	55208981	55209209
+chrX	55209656	55210007
+chrX	58330489	58330844
+chrX	58373807	58373963
+chrX	58377681	58377865
+chrX	58415351	58416388
+chrX	58432412	58432681
+chrX	58485888	58486242
+chrX	58488899	58494529
+chrX	58499467	58504236
+chrX	58506077	58528215
+chrX	58528185	58536884
+chrX	58544062	58582416
+chrX	61681835	61919684
+chrX	62003206	62041581
+chrX	83658930	83659020
+chrX	108297349	108297887
+chrX	114959058	115006438
+chrX	125605624	125607352
+chrX	125714986	125715339
+chrX	125864845	125864981
+chrX	125865720	125865875
+chrY	313471	313614
+chrY	3004990	3005176
+chrY	4212808	4212911
+chrY	7671818	7694929
+chrY	7726065	7730230
+chrY	7730735	7731599
+chrY	7735812	7752888
+chrY	7785068	7806312
+chrY	7806857	7814705
+chrY	7815231	7820479
+chrY	7829938	7832033
+chrY	7832745	7848696
+chrY	7870344	7873583
+chrY	7874116	7874585
+chrY	7875410	7885258
+chrY	7886546	7894592
+chrY	7898928	7916813
+chrY	7918791	7921353
+chrY	7926345	7936706
+chrY	7941131	7947439
+chrY	7948791	7964449
+chrY	8179011	8181144
+chrY	8181758	8213331
+chrY	8214630	8215638
+chrY	8220422	8230062
+chrY	8230687	8231547
+chrY	8240773	8265917
+chrY	8291536	8292943
+chrY	8294003	8295176
+chrY	8296945	8321376
+chrY	8325814	8325930
+chrY	8326679	8333467
+chrY	8334028	8342388
+chrY	8356545	8369347
+chrY	8909561	8909926
+chrY	8979479	8979586
+chrY	9072782	9072994
+chrY	9908431	9925609
+chrY	9981953	9982127
+chrY	10034865	10036713
+chrY	10040628	10045658
+chrY	10047774	10052534
+chrY	10053696	10057723
+chrY	10059395	10073695
+chrY	10075083	10075782
+chrY	10080737	10104540
+chrY	13104531	13144369
+chrY	13193967	13196536
+chrY	13252194	13259485
+chrY	13290178	13290668
+chrY	13445958	13490592
+chrY	13642187	13749785
+chrY	13798523	13870985
+chrY	19691914	19692525
+chrY	19764064	19776199
+chrY	19780601	19781705
+chrY	19783670	19796397
+chrY	19800069	19801420
+chrY	19808086	19817101
+chrY	19944299	19944582
+chrY	20235196	20235479
+chrY	20362680	20371695
+chrY	20378361	20379712
+chrY	20383384	20396111
+chrY	20398076	20399180
+chrY	20403582	20415714
+chrY	20487249	20487860
+chrY	23124789	23125578
+chrY	23149028	23151206
+chrY	23157970	23158246
+chrY	23159002	23167738
+chrY	23178887	23181771
+chrY	23220741	23223626
+chrY	23234126	23235823
+chrY	23236899	23248081
+chrY	23248730	23248852
+chrY	23899296	23899389
+chrY	23956450	23956629
+chrY	24247660	24247701
+chrY	24631000	24631041
+chrY	24953160	24975658
+chrY	24980998	24991236
+chrY	25022754	25039186
+chrY	25040154	25042422
+chrY	25048333	25059259
+chrY	25060236	25064799
+chrY	25099140	25121883
+chrY	25122420	25160801
+chrY	25182405	25192373
+chrY	25217723	25219410
+chrY	25493589	25495276
+chrY	26148316	26148451
+chrY	26586906	26609406
+chrY	26614746	26624984
+chrY	26656503	26672935
+chrY	26673903	26676171
+chrY	26682082	26693008
+chrY	26693985	26698548
+chrY	26732884	26755624
+chrY	26756161	26794539
+chrY	26816149	26826117
+chrY	26851467	26853154
+chrY	27109248	27110935
+chrY	27136282	27146250
+chrY	27167860	27206242
+chrY	27206779	27229503
+chrY	27263849	27268412
+chrY	27269389	27280316
+chrY	27286227	27288495
+chrY	27289463	27305896
+chrY	27337416	27347657
+chrY	27352997	27375498
+chrY	27813985	27814120
+chrY	28555027	28555354
+chrY	28784130	28819696
+chrY	58819368	58917649
+chrY	58971914	58997783
+chrY	59361268	59362786
diff --git a/assets/blacklists/GRCm38-blacklist.bed b/assets/blacklists/GRCm38-blacklist.bed
old mode 100755
new mode 100644
index 3699d020..fadce809
--- a/assets/blacklists/GRCm38-blacklist.bed
+++ b/assets/blacklists/GRCm38-blacklist.bed
@@ -1,164 +1,559 @@
-10	3110060	3110270
-10	22142530	22142880
-10	22142830	22143070
-10	58223870	58224100
-10	58225260	58225500
-10	58228320	58228520
-11	3148660	3148860
-11	3154960	3155170
-11	3158530	3158750
-11	3161780	3161990
-11	3167020	3167250
-11	3169390	3169620
-11	3172450	3172670
-11	3172950	3173190
-11	3184190	3185750
-11	3185700	3186360
-11	3186330	3189230
-11	3189190	3190740
-11	3190750	3191000
-11	3190960	3194430
-11	3194400	3195310
-11	3195240	3197220
-11	3197340	3197950
-11	3197890	3198700
-11	3198630	3199440
-11	3199350	3200120
-11	54139940	54140230
-11	54140470	54140740
-11	88967720	88969600
-11	88969850	88970350
-11	109011550	109012090
-12	3109920	3110150
-12	105436040	105436270
-13	3372960	3373380
-13	3373410	3373630
-13	77438870	77439090
-13	97190460	97190690
-13	99790830	99791090
-13	119488570	119489320
-13	119597600	119598320
-13	119599860	119600050
-13	119601360	119601600
-13	119601800	119602210
-13	119602360	119602580
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\ No newline at end of file
diff --git a/assets/blacklists/GRCm39-blacklist.bed b/assets/blacklists/GRCm39-blacklist.bed
new file mode 100644
index 00000000..78a64551
--- /dev/null
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\ No newline at end of file
diff --git a/assets/blacklists/hg38-blacklist.bed b/assets/blacklists/hg38-blacklist.bed
index c3e00911..61b6e46a 100644
--- a/assets/blacklists/hg38-blacklist.bed
+++ b/assets/blacklists/hg38-blacklist.bed
@@ -1,38 +1,1049 @@
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\ No newline at end of file
diff --git a/assets/blacklists/mm10-blacklist.bed b/assets/blacklists/mm10-blacklist.bed
old mode 100755
new mode 100644
index 8c71cd3b..b5ae050b
--- a/assets/blacklists/mm10-blacklist.bed
+++ b/assets/blacklists/mm10-blacklist.bed
@@ -1,164 +1,559 @@
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diff --git a/assets/blacklists/mm39-blacklist.bed b/assets/blacklists/mm39-blacklist.bed
new file mode 100644
index 00000000..373ab856
--- /dev/null
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+chr13	110879502	110882082
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+chr17	4675442	4677879
+chr17	13523841	13527624
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+chr17	13804984	13812864
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+chr17	23094249	23096858
+chr17	29320413	29328488
+chr17	36541116	36543498
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+chr17	68047302	68049631
+chr17	84768116	84772088
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diff --git a/conf/igenomes.config b/conf/igenomes.config
index d2c9e4c3..8da96bcb 100644
--- a/conf/igenomes.config
+++ b/conf/igenomes.config
@@ -34,7 +34,7 @@ params {
             bed12       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed"
             mito_name   = "chrM"
             macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
+            blacklist   = "${projectDir}/assets/blacklists/GCRh38-blacklist.bed"
         }
         'CHM13' {
             fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa"