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 1/2] 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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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"

From e93b4520073c6fe0946c1f4bbcb39e933cf1c00f Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Thu, 31 Aug 2023 16:33:12 +0100
Subject: [PATCH 2/2] Update changelog

---
 CHANGELOG.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c34d3946..df1d3440 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,11 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [3.2] - 2023-06-15
+## [3.2] - 2023-08-31
 
 ### Major Changes
 
 - [[#189](https://github.com/nf-core/cutandrun/pull/189)] - Duplicates arising from linear amplification can be now removed by setting `--remove_linear_duplicates true`. `false` is default. [Linear amplification](https://doi.org/10.1186/1471-2164-4-19) is used in the [TIPseq protocol](https://doi.org/10.1083/jcb.202103078) in which genomic DNA is cut with Tn5 loaded with T7 promoter sequence that gets inserted in the cut DNA fragment. The T7 promoter sequence is then used to perform in vitro transcription to produce copies of the cut fragment. These duplicates are referred to as linear duplicates. Recent iterations of the CUT&Tag protocol, such as [nano-CUT&Tag](https://doi.org/10.1038/s41587-022-01535-4), have also been modified to include a linear amplification step. Credit to teemuronkko for this.
+- [[#208](https://github.com/nf-core/cutandrun/issues/208)] - Updated the genome blacklists file to more accurate CUT&RUN specific regions rather than the old ChIP-Seq ENCODE blacklist. This should improve mapping rates and reduce spurious peaks. Credit to Adrija K for this. [[The CUT&RUN suspect list of problematic regions of the genome](https://doi.org/10.1186/s13059-023-03027-3)]
 
 ### Enhancements