updated COLOC and eCAVIAR code

README.md

@@ -1,7 +1,7 @@
 [![DOI](https://zenodo.org/badge/268661500.svg)](https://zenodo.org/badge/latestdoi/268661500)
 
 # Developing brain mega xQTL
-**Supplemental tables, all QTL summary statistics, and other extended data are available at https://doi.org/10.7303/syn50897018.5**
+**All QTL summary statistics, and other extended data are available at https://doi.org/10.7303/syn50897018.5**
 ## 1: Munging data
 ## 2: Genotype
 ### 2-1: Pre-imputation
@@ -80,6 +80,7 @@ write.table(txi.tx$abundance,file="tx.TPM.tsv",quote=FALSE, sep='\t')
 - `apex_analysis.ipynb`
 - `Snakefile`
 ## 5: Integrative analysis
+**See `coloc_ecaviar_May_2024/` for colocalization analysis**
 ### 5-1: sLDSC 
 - `ldsc_analysis.ipynb`
 - `Snakefile`

code/05-QTL-GWAS/coloc_ecaviar_May_2024/ADHD.Demontis.2019_loci.tsv

@@ -0,0 +1,12 @@
+locus	CHR	BP  SNP
+1	1	44184192    rs11420276
+2	1	96602440    rs1222063
+3	3	20669071    rs4858241
+4	4	31151456    rs28411770
+5	5	87854395    rs4916723
+6	7	114086133   rs5886709
+7	8	34352610    rs74760947
+8	10	106747354   rs11591402
+9	12	89760744    rs1427829
+10	15	47754018    rs281324
+11	16	72578131    rs212178

code/05-QTL-GWAS/coloc_ecaviar_May_2024/ALZ.Bellenguez.2022_loci.tsv

@@ -0,0 +1,84 @@
+locus	SNP	CHR	BP	Gene	Known_locus	Minor_major	MAF	OR_minor	CI_95	P
+1	rs679515	1	207577223	CR1	CR1	T/C	0.188	1.13	1.11–1.15	7.2 × 10−46
+2	rs6733839	2	127135234	BIN1	BIN1	T/C	0.389	1.17	1.16–1.19	6.1 × 10−118
+3	rs10933431	2	233117202	INPP5D	INPP5D	G/C	0.234	0.93	0.92–0.95	3.6 × 10−18
+4	rs6846529	4	11023507	CLNK	CLNK/HS3ST1	C/T	0.283	1.07	1.05–1.08	2.2 × 10−17
+5	rs6605556	6	32615322	HLA-DQA1	HLA	G/A	0.161	0.91	0.90–0.93	7.1 × 10−20
+6	rs10947943	6	41036354	UNC5CL	TREM2	A/G	0.142	0.94	0.93–0.96	1.1 × 10−9
+7	rs143332484	6	41161469	TREM2	TREM2	T/C	0.013	1.41	1.32–1.50	2.8 × 10−25
+8	rs75932628	6	41161514	TREM2	TREM2	T/C	0.003	2.39	2.09–2.73	2.5 × 10−37
+9	rs60755019	6	41181270	TREML2	TREM2	G/A	0.004	1.55	1.33–1.80	2.1 × 10−8
+10	rs7767350	6	47517390	CD2AP	CD2AP	T/C	0.271	1.08	1.06–1.09	7.9 × 10−22
+11	rs6966331	7	37844191	EPDR1	NME8	T/C	0.349	0.96	0.94–0.97	4.6 × 10−10
+12	rs7384878	7	100334426	SPDYE3	ZCWPW1/NYAP1	C/T	0.31	0.92	0.91–0.94	1.1 × 10−26
+13	rs11771145	7	143413669	EPHA1	EPHA1	A/G	0.348	0.95	0.93–0.96	3.3 × 10−14
+14	rs73223431	8	27362470	PTK2B	PTK2B	T/C	0.369	1.07	1.06–1.08	4.0 × 10−22
+15	rs11787077	8	27607795	CLU	CLU	T/C	0.392	0.91	0.90–0.92	1.7 × 10−44
+16	rs7912495	10	11676714	USP6NL	ECHDC3	G/A	0.462	1.06	1.05–1.08	9.7 × 10−19
+17	rs10437655	11	47370397	SPI1	CELF1/SPI1	A/G	0.399	1.06	1.04–1.07	5.3 × 10−14
+18	rs1582763	11	60254475	MS4A4A	MS4A	A/G	0.371	0.91	0.90–0.92	3.7 × 10−42
+19	rs3851179	11	86157598	EED	PICALM	T/C	0.358	0.9	0.89–0.92	3.0 × 10−48
+20	rs74685827	11	121482368	SORL1	SORL1	G/T	0.019	1.19	1.13–1.25	2.8 × 10−11
+21	rs11218343	11	121564878	SORL1	SORL1	C/T	0.039	0.84	0.81–0.87	1.4 × 10−21
+22	rs17125924	14	52924962	FERMT2	FERMT2	G/A	0.089	1.1	1.07–1.12	8.3 × 10−16
+23	rs7401792	14	92464917	SLC24A4	SLC24A4/RIN3	G/A	0.371	1.04	1.02–1.05	4.8 × 10−8
+24	rs12590654	14	92472511	SLC24A4	SLC24A4/RIN3	A/G	0.328	0.93	0.92–0.95	4.2 × 10−21
+25	rs8025980	15	50701814	SPPL2A	SPPL2A	G/A	0.345	0.96	0.94–0.97	1.3 × 10−8
+26	rs602602	15	58764824	MINDY2	ADAM10	A/T	0.28	0.94	0.93–0.96	2.1 × 10−15
+27	rs117618017	15	63277703	APH1B	APH1B	T/C	0.144	1.11	1.09–1.13	2.2 × 10−25
+28	rs889555	16	31111250	BCKDK	KAT8	T/C	0.281	0.95	0.94–0.97	2.0 × 10−11
+29	rs4985556	16	70660097	IL34	IL34	A/C	0.115	1.07	1.05–1.09	6.0 × 10−10
+30	rs12446759	16	81739398	PLCG2	PLCG2	G/A	0.403	0.95	0.94–0.96	1.2 × 10−13
+31	rs72824905	16	81908423	PLCG2	PLCG2	G/C	0.008	0.74	0.68–0.81	8.5 × 10−12
+32	rs7225151	17	5233752	SCIMP	SCIMP/RABEP1	A/G	0.124	1.08	1.05–1.10	4.1 × 10−13
+33	rs199515	17	46779275	WNT3	MAPT	G/C	0.219	0.94	0.93–0.96	9.3 × 10−13
+34	rs616338	17	49219935	ABI3	ABI3	T/C	0.012	1.32	1.23–1.42	2.8 × 10−14
+35	rs2526377	17	58332680	TSPOAP1	TSPOAP1	G/A	0.445	0.95	0.94–0.97	1.6 × 10−12
+36	rs4277405	17	63471557	ACE	ACE	C/T	0.384	0.94	0.93–0.95	8.8 × 10−20
+37	rs12151021	19	1050875	ABCA7	ABCA7	A/G	0.336	1.1	1.09–1.12	1.6 × 10−37
+38	rs6014724	20	56423488	CASS4	CASS4	G/A	0.09	0.89	0.87–0.91	4.1 × 10−21
+39	rs2830489	21	26775872	ADAMTS1	ADAMTS1	T/C	0.281	0.95	0.94–0.97	1.7 × 10−10
+40	rs141749679	1	109345810	SORT1	NA	C/T	0.004	1.38	1.24–1.54	7.5 × 10−9
+41	rs72777026	2	9558882	ADAM17	NA	G/A	0.144	1.06	1.04–1.08	2.7 × 10−8
+42	rs17020490	2	37304796	PRKD3	NA	C/T	0.145	1.06	1.04–1.08	3.3 × 10−9
+43	rs143080277	2	105749599	NCK2	NA	C/T	0.005	1.47	1.33–1.63	2.1 × 10−13
+44	rs139643391	2	202878716	WDR12	NA	T/TC	0.131	0.94	0.92–0.96	1.1 × 10−8
+45	rs16824536	3	155069722	MME	NA	A/G	0.054	0.92	0.89–0.95	3.6 × 10−8
+46	rs61762319	3	155084189	MME	NA	G/A	0.026	1.16	1.11–1.21	2.2 × 10−11
+47	rs3822030	4	993555	IDUA	NA	G/T	0.429	0.95	0.94–0.96	8.3 × 10−12
+48	rs2245466	4	40197226	RHOH	NA	G/C	0.343	1.05	1.03–1.06	1.2 × 10−9
+49	rs112403360	5	14724304	ANKH	NA	A/T	0.073	1.09	1.06–1.12	2.3 × 10−9
+50	rs62374257	5	86927378	COX7C	NA	C/T	0.23	1.07	1.05–1.09	1.4 × 10−15
+51	rs871269	5	151052827	TNIP1	NA	T/C	0.326	0.96	0.95–0.97	8.7 × 10−9
+52	rs113706587	5	180201150	RASGEF1C	NA	A/G	0.11	1.09	1.07–1.12	2.2 × 10−16
+53	rs785129	6	114291731	HS3ST5	NA	T/C	0.35	1.04	1.03–1.06	2.4 × 10−9
+54	rs6943429	7	7817263	UMAD1	NA	T/C	0.42	1.05	1.03–1.06	1.0 × 10−10
+55	rs10952097	7	8204382	ICA1	NA	T/C	0.114	1.07	1.05–1.10	6.8 × 10−9
+56	rs13237518	7	12229967	TMEM106B	NA	A/C	0.411	0.96	0.94–0.97	4.9 × 10−11
+57	rs1160871	7	28129126	JAZF1	NA	G/GTCTT	0.222	0.95	0.93–0.97	9.8 × 10−9
+58	rs76928645	7	54873635	SEC61G	NA	T/C	0.103	0.93	0.91–0.95	1.6 × 10−10
+59	rs1065712	8	11844613	CTSB	NA	C/G	0.053	1.09	1.06–1.12	1.9 × 10−9
+60	rs34173062	8	144103704	SHARPIN	NA	A/G	0.081	1.13	1.09–1.16	1.7 × 10−16
+61	rs1800978	9	104903697	ABCA1	NA	G/C	0.13	1.06	1.04–1.08	1.6 × 10−9
+62	rs7068231	10	60025170	ANK3	NA	T/G	0.403	0.95	0.94–0.96	3.3 × 10−13
+63	rs6586028	10	80494228	TSPAN14	NA	C/T	0.196	0.93	0.91–0.94	2.0 × 10−19
+64	rs6584063	10	96266650	BLNK	NA	G/A	0.043	0.89	0.86–0.92	6.7 × 10−11
+65	rs7908662	10	122413396	PLEKHA1	NA	G/A	0.467	0.96	0.95–0.97	2.6 × 10−9
+66	rs6489896	12	113281983	TPCN1	NA	C/T	0.076	1.08	1.05–1.10	1.8 × 10−9
+67	rs7157106	14	105761758	IGH_gene_cluster	NA	A/G	0.36	1.05	1.03–1.07	2.0 × 10−8
+68	rs10131280	14	106665591	IGH_gene_cluster	NA	A/G	0.133	0.94	0.92–0.96	4.3 × 10−10
+69	rs3848143	15	64131307	SNX1	NA	G/A	0.22	1.05	1.04–1.07	8.4 × 10−11
+70	rs12592898	15	78936857	CTSH	NA	A/G	0.133	0.94	0.92–0.96	4.2 × 10−9
+71	rs1140239	16	30010081	DOC2A	NA	T/C	0.379	0.94	0.93–0.96	2.6 × 10−13
+72	rs450674	16	79574511	MAF	NA	C/T	0.373	0.96	0.95–0.98	3.2 × 10−8
+73	rs16941239	16	86420604	FOXF1	NA	A/T	0.029	1.13	1.08–1.17	1.3 × 10−8
+74	rs56407236	16	90103687	PRDM7	NA	A/G	0.069	1.11	1.08–1.14	6.5 × 10−15
+75	rs35048651	17	1728046	WDR81	NA	T/TGAG	0.214	1.06	1.04–1.08	7.7 × 10−11
+76	rs2242595	17	18156140	MYO15A	NA	A/G	0.112	0.94	0.92–0.96	1.1 × 10−9
+77	rs5848	17	44352876	GRN	NA	T/C	0.289	1.07	1.06–1.09	2.4 × 10−20
+78	rs149080927	19	1854254	KLF16	NA	G/GC	0.48	1.05	1.04–1.07	5.1 × 10−10
+79	rs9304690	19	49950060	SIGLEC11	NA	T/C	0.24	1.05	1.03–1.07	4.7 × 10−9
+80	rs587709	19	54267597	LILRB2	NA	C/T	0.325	1.05	1.04–1.07	3.6 × 10−11
+81	rs1358782	20	413334	RBCK1	NA	A/G	0.246	0.95	0.94–0.97	1.6 × 10−8
+82	rs6742	20	63743088	SLC2A4RG	NA	T/C	0.221	0.95	0.93–0.97	2.6 × 10−9
+83	rs2154481	21	26101558	APP	NA	C/T	0.476	0.95	0.94–0.97	1.0 × 10−12

code/05-QTL-GWAS/coloc_ecaviar_May_2024/ALZ.Jansen.2019_loci.tsv

@@ -0,0 +1,30 @@
+locus	CHR	Gene	SNP	BP	A1	A2	Z	P
+1	1	ADAMTS4	rs4575098	161155392	A	G	6.36	2.05 × 10−10
+2	1	CR1	rs2093760	207786828	A	G	8.82	1.10 × 10−18
+3	2	BIN1	rs4663105	127891427	C	A	13.94	3.38 × 10−44
+4	2	INPPD5	rs10933431	233981912	G	C	−6.13	8.92 × 10−10
+5	3	HESX1	rs184384746	57226150	T	C	5.69	1.24 × 10−8
+6	4	CLNK	rs6448453	11026028	A	G	6	1.93 × 10−9
+7	6	HLA-DRB1	rs6931277	32583357	T	A	−6.49	8.41 × 10−11
+8	6	TREM2	rs187370608	40942196	A	G	8.26	1.45 × 10−16
+9	6	CD2AP	rs9381563	47432637	C	T	6.33	2.52 × 10−10
+10	7	ZCWPW1	rs1859788	99971834	A	G	−7.93	2.22 × 10−15
+11	7	EPHA1	rs7810606	143108158	T	C	−6.62	3.59 × 10−11
+12	7	CNTNAP2	rs114360492	145950029	T	C	5.99	2.10 × 10−9
+13	8	CLU/PTK2B	rs4236673	27464929	A	G	−8.98	2.61 × 10−19
+14	10	ECHDC3	rs11257238	11717397	C	T	5.69	1.26 × 10−8
+15	11	MS4A6A	rs2081545	59958380	A	C	−7.97	1.55 × 10−15
+16	11	PICALM	rs867611	85776544	G	A	−8.75	2.19 × 10−18
+17	11	SORL1	rs11218343	121435587	C	T	−6.79	1.09 × 10−11
+18	14	SLC24A4	rs12590654	92938855	A	G	−6.39	1.65 × 10−10
+19	15	ADAM10	rs442495	59022615	C	T	−6.07	1.31 × 10−9
+20	15	APH1B	rs117618017	63569902	T	C	5.52	3.35 × 10−8
+21	16	KAT8	rs59735493	31133100	A	G	−5.49	3.98 × 10−8
+22	17	SCIMP	rs113260531	5138980	A	G	6.12	9.16 × 10−10
+23	17	ABI3	rs28394864	47450775	A	G	5.62	1.87 × 10−8
+24	18	ALPK2	rs76726049	56189459	C	T	5.52	3.30 × 10−8
+25	19	ABCA7	rs111278892	1039323	G	C	6.5	7.93 × 10−11
+26	19	APOE	rs41289512	45351516	G	C	35.5	5.79 × 10−276
+27	19	AC074212.3	rs76320948	46241841	T	C	5.46	4.64 × 10−8
+28	19	CD33	rs3865444	51727962	A	C	−5.81	6.34 × 10−9
+29	20	CASS4	rs6014724	54998544	G	A	−6.18	6.56 × 10−10

code/05-QTL-GWAS/coloc_ecaviar_May_2024/ASD.iPSYCHPGC.2018_loci.tsv

@@ -0,0 +1,4 @@
+locus	CHR	BP	SNP
+1	20	21248116	rs910805
+2	8	10576775	rs10099100
+3	20	14836243	rs10099100

code/05-QTL-GWAS/coloc_ecaviar_May_2024/MDD.Howard.PGC.2019_loci.tsv

@@ -0,0 +1,102 @@
+locus	CHR	BP	SNP
+1	1	72765116	rs2568958
+2	13	53647048	rs1343605
+3	5	164523472	rs11135349
+4	5	103972357	rs30266
+5	18	53099012	rs12967143
+6	10	106610839	rs1021363
+7	11	88744425	rs7932640
+8	1	73668836	rs10890020
+9	5	87545318	rs3099439
+10	7	12253880	rs2043539
+11	14	104017953	rs10149470
+12	3	157977962	rs1095626
+13	1	197704717	rs17641524
+14	14	42074726	rs61990288
+15	1	175913828	rs10913112
+16	14	75130235	rs1045430
+17	18	35138245	rs12967855
+18	1	8489302	rs301799
+19	11	113370758	rs61902811
+20	16	13755530	rs56887639
+21	9	36999369	rs7030813
+22	1	37192741	rs1002656
+23	16	13066833	rs7200826
+24	2	58012833	rs1568452
+25	18	52751639	rs12966052
+26	22	41487218	rs5995992
+27	9	11513019	rs1982277
+28	18	50731802	rs7227069
+29	7	109099919	rs58104186
+30	7	117502574	rs7807677
+31	1	52342427	rs1890946
+32	9	119731045	rs10817969
+33	15	37643831	rs8037355
+34	16	7666402	rs7198928
+35	1	177428018	rs72710803
+36	6	66565703	rs9363467
+37	5	93071630	rs10061069
+38	9	23737627	rs3793577
+39	9	126634255	rs2670139
+40	6	142996618	rs2876520
+41	6	105365891	rs1933802
+42	18	77580712	rs7241572
+43	12	84465022	rs56314503
+44	11	61471678	rs198457
+45	9	17016503	rs263645
+46	13	99115041	rs4772087
+47	16	6315880	rs7193263
+48	2	22503044	rs12052908
+49	6	101387304	rs7758630
+50	1	50559162	rs11579246
+51	14	64697037	rs1152578
+52	2	208044470	rs62188629
+53	3	44736493	rs4346585
+54	12	121205078	rs3213572
+55	3	61192911	rs141954845
+56	13	66941792	rs9592461
+57	8	71347626	rs67436663
+58	11	30892824	rs1448938
+59	16	21639710	rs12923444
+60	4	131237381	rs35553410
+61	13	31907741	rs1409379
+62	18	52488672	rs62091461
+63	7	2110346	rs3823624
+64	9	31124452	rs34653192
+65	20	39997404	rs143186028
+66	8	65562019	rs7837935
+67	2	157111313	rs1226412
+68	7	82454404	rs2247523
+69	13	80826373	rs9545360
+70	15	47684936	rs34488670
+71	3	49214066	rs13084037
+72	9	2983774	rs1354115
+73	11	70544937	rs7117514
+74	20	44680853	rs12624433
+75	7	82936909	rs16887442
+76	11	57650796	rs2509805
+77	9	25232978	rs59283172
+78	4	177350956	rs7659414
+79	6	165121844	rs2029865
+80	5	61509655	rs60157091
+81	11	65314830	rs58621819
+82	11	127022560	rs57344483
+83	4	123186393	rs45510091
+84	1	80809636	rs113188507
+85	6	147950422	rs725616
+86	14	60141822	rs1956373
+87	9	120484009	rs913930
+88	4	3207142	rs7685686
+89	2	86819128	rs7585722
+90	3	117509984	rs6783233
+91	1	181740924	rs169235
+92	17	27363750	rs75581564
+93	12	23987925	rs78337797
+94	12	110741356	rs10774600
+95	11	118713180	rs2187490
+96	3	53244151	rs7624336
+97	1	37709328	rs1466887
+98	4	42110353	rs34937911
+99	1	67146817	rs10789214
+100	10	1795194	rs997934
+101	19	30939989	rs33431