linkage-analysis~manhattan-plot

input_1:genotype vcf

input_1/all.hiquality.100k.vcf

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	r100	r101	r102	r103	r104	r105	r106	r107	r108	r109	r110	r111	r112	r113	r114	r115	r116	r117	r118	r119	r120	r121	r122	r123	r124	r125	r126	r127	r128	r129	r130	r131	r132	r133	r134	r135	r136	r137	r138	r139	r140	r141	r142	r143	r144	r145	r146	r147	r148	r149	r150	r151	r152	r153	r154	r155	r156	r157	r158	r159	r171	r172	r173	r174	r175	r176	r177	r178	r179	r180	r181	r182	r183	r184	r185	r186	r187	r188	r189	r190	r191	r192	r193	r194	r195	r196	r197	r198	r199	r200	r201	r202	r203	r204	r205	r206	r207	r208	r209	r210	r211	r212	r213	r214	r215	r216	r217	r218	r219	r220	r221	r222	r223	r224	r225	r226	r227	r228	r229	r230	r231	r232	r233	r234	r235	r236	r237	r238	r239	r240	r241	r242	r243	r244	r245	r246	r247	r248	r249	r250	r251	r252	r253	r254	r255	r256	r257	r258	r259	r260	r261	r262	r263	r264	r265	r266	r267	r268	r269	r270	r271	r272	r273	r274	r275	r276	r277	r278	r279	r42	r43	r44	r45	r46	r47	r48	r49	r50	r51	r52	r53	r54	r55	r56	r57	r58	r59	r60	r61	r62	r63	r64	r65	r66	r67	r68	r69	r70	r71	r72	r73	r74	r75	r76	r77	r78	r79	r80	r81	r82	r83	r84	r85	r86	r87	r88	r89	r90	r91	r92	r93	r94	r95	r96	r97	r98	r99
NC_035081.1	31143	.	C	CAGCCGTCT	72.67	.	AC=1;AF=2.212e-03;AN=452;BaseQRankSum=0.00;DP=2780;ExcessHet=3.0103;FS=26.527;InbreedingCoeff=-0.0017;MLEAC=1;MLEAF=2.212e-03;MQ=52.38;MQRankSum=2.05;QD=5.59;ReadPosRankSum=3.58;SOR=0.576	GT:AD:DP:GQ:PGT:PID:PL:PS	0/0:9,0:9:27:.:.:0,27,311	0/0:19,0:19:57:.:.:0,57,810	0/0:11,0:11:33:.:.:0,33,447	0/0:19,0:19:57:.:.:0,57,743	0/0:11,0:11:33:.:.:0,33,405	0/0:16,0:16:48:.:.:0,48,582	0/0:12,0:12:36:.:.:0,36,489	0/0:9,0:9:27:.:.:0,27,327	0/0:19,0:19:57:.:.:0,57,854	0/0:8,0:8:24:.:.:0,24,287	0/0:11,0:11:33:.:.:0,33,443	0/0:15,0:15:45:.:.:0,45,584	0/0:12,0:12:36:.:.:0,36,496	0/0:15,0:15:45:.:.:0,45,588	0/0:10,0:10:30:.:.:0,30,346	0/0:11,0:11:33:.:.:0,33,368	0/0:11,0:11:33:.:.:0,33,385	0/0:16,0:16:42:.:.:0,42,630	0/0:22,0:22:66:.:.:0,66,947	0/0:12,0:12:36:.:.:0,36,501	0/0:15,0:15:45:.:.:0,45,605	0/0:21,0:21:63:.:.:0,63,876	0/0:17,0:17:51:.:.:0,51,682	0/0:16,0:16:48:.:.:0,48,594	0/0:8,0:8:24:.:.:0,24,306	0/0:17,0:17:51:.:.:0,51,723	0/0:22,0:22:66:.:.:0,66,719	0/0:9,0:9:27:.:.:0,27,307	0/0:10,0:10:30:.:.:0,30,361	0/0:10,0:10:30:.:.:0,30,302	0/0:24,0:24:72:.:.:0,72,896	0/0:27,0:27:81:.:.:0,81,1058	0/0:5,0:5:15:.:.:0,15,173	0/0:19,0:19:57:.:.:0,57,817	0/0:22,0:22:66:.:.:0,66,814	0/0:16,0:18:48:.:.:0,48,688	0/0:3,0:3:9:.:.:0,9,89	0/0:14,0:14:42:.:.:0,42,522	0/0:5,0:5:15:.:.:0,15,201	0/0:3,0:3:9:.:.:0,9,91	0/0:20,0:20:60:.:.:0,60,807	0/0:27,0:27:81:.:.:0,81,1077	0/0:10,0:10:30:.:.:0,30,378	0/0:2,0:2:6:.:.:0,6,53	0|1:10,3:13:96:0|1:31143_C_CAGCCGTCT:96,0,411:31143	0/0:1,0:1:3:.:.:0,3,16	0/0:5,0:5:15:.:.:0,15,157	0/0:11,0:11:33:.:.:0,33,461	0/0:4,0:4:12:.:.:0,12,174	0/0:12,0:12:36:.:.:0,36,450	0/0:5,0:5:15:.:.:0,15,139	0/0:9,0:9:27:.:.:0,27,372	0/0:3,0:3:9:.:.:0,9,85	0/0:5,0:5:15:.:.:0,15,161	0/0:41,0:41:99:.:.:0,107,1631	0/0:30,0:30:90:.:.:0,90,1211	0/0:13,0:13:39:.:.:0,39,490	0/0:5,0:5:15:.:.:0,15,167	0/0:8,0:8:24:.:.:0,24

input_2:phenotype information

input_2/phenotype.txt

r100	HT
r101	HT
r102	HT
r103	HT
r104	HT
r105	HT
r106	HT
r107	HT
r108	HT
r109	HT

input_3:reference genome file

input_3/GCF_002163495.1_Omyk_1.0_genomic.fna

>NC_035077.1 Oncorhynchus mykiss isolate Swanson chromosome 1, Omyk_1.0, whole genome shotgun sequence
TGGGGGTGGATGGTCTGACTGGTGGTGGGGGTGGATGGTTTGACTGGTAGTGGTGGTGGATGGTCTGACTGGTAGTGGTG
GTGGAGGGTCTGACTGGTAGTGGTGGTGGAGGGTCTGACTGGTGGTGGAGGGTCTGACAGCTATCACAGCCCGGTCCTCT
TTCCTACTGGCCTCCACTATAACCAGTCACAGCCCTGTCTTCCTCCTTCCTACCGGCCTCCACTATAACCAGTCACAGCC
CAGTCCTCCTCCTTCCTACTGGCCTCCACTATAACCAGTCACAGCCCAGTCCTCCTTCCTACTGCCTCCACTATAACTAG
TCACAGCCCAGTCCTCTTTCCTACTGGCCTCCACTATAACCTCCACTATAACTAGTCACAGCCCAGTGTGAAGTACATAC
GATAGGCTAAAAGTTTCCATGCAACAGCTTGTTTGGGTAAcgttgtcatgacgtggccctctttgcCTATAACAAGCACC
AACTTTCTCTCACGCaaacctctctcttccccctacacACCCAGGCTCTGaaatctcaggtcgtaaattcctggaggaaa
TTCTCTTCCCGTCCATGCAGTATAGAGAGAGggttcacagtagaacaaaggaacttcttctacctcacagaacttgataa
ctgaacaatgtccatgttttggagaatgtgtaaacggtcggtggCGAATCCAGCTACGACCCGGGCCATTTTGTTTTATG

Option

Output

input_1/all.hiquality.100k.vcf.GQ20.DP5.rm0.4.hetero.HT2.png

input_1/all.hiquality.100k.vcf.GQ20.DP5.rm0.4.homo.HT2.png

input_1/all.hiquality.100k.vcf.GQ20.DP5.rm0.4.sp.HT2.png