(samplot) norman@norman-HP-Z820-Workstation:/mnt/data/norman/Analysis/banana/dysgu-Analysis$ samplot vcf --debug --filter "SVTYPE == 'TRA'" --vcf S30GY_01-vs-SA_GN.vcf -d all-plots/ -O png -b /home/norman/data/Analysis/banana/TR4_SEQ2020/Analysis-Jul2023/dna-proto-workflow/output/alignments/samples/bwa/Baxijiao-AAA-T2T-genome/S30GY_01.bam /home/norman/data/Analysis/banana/TR4_SEQ2020/Analysis-Jul2023/dna-proto-workflow/output/alignments/samples/bwa/Baxijiao-AAA-T2T-genome/SA_GN.bam > samplot_commands.sh
samplot_vcf - DEBUG: No samples pass filters for INV at chr01:2497853-2497940
samplot_vcf - DEBUG: No samples pass filters for INV at chr01:13577578-13577753
samplot_vcf - DEBUG: Skipping INS at chr01:15771785-15771786, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for DEL at chr01:24448305-24448494
samplot_vcf - DEBUG: No samples pass filters for INV at chr01:28907545-28908026
samplot_vcf - DEBUG: Skipping INS at chr01:30560624-30560719, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for DEL at chr01:30672736-30672768
samplot_vcf - DEBUG: Skipping INS at chr01:32624369-32624370, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr01:34872528-34872939
samplot_vcf - DEBUG: No samples pass filters for INV at chr01:35661076-35661268
samplot_vcf - DEBUG: No samples pass filters for INV at chr02:1106654-1106715
samplot_vcf - DEBUG: No samples pass filters for DEL at chr02:19962734-19962783
samplot_vcf - DEBUG: No samples pass filters for DEL at chr02:20292788-20292834
samplot_vcf - DEBUG: No samples pass filters for INV at chr03:12995518-12995662
samplot_vcf - DEBUG: No samples pass filters for INV at chr03:15335529-15335822
samplot_vcf - DEBUG: Skipping INS at chr03:18394490-18394492, INS type not supported
samplot_vcf - DEBUG: Skipping INS at chr03:18455527-18455528, INS type not supported
samplot_vcf - DEBUG: Skipping INS at chr03:26071683-26071684, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr03:26360615-26360811
samplot_vcf - DEBUG: No samples pass filters for INV at chr03:27004173-27004389
samplot_vcf - DEBUG: No samples pass filters for INV at chr03:31054813-31054976
samplot_vcf - DEBUG: No samples pass filters for INV at chr03:38792047-38792354
samplot_vcf - DEBUG: No samples pass filters for INV at chr03:45537292-45537367
samplot_vcf - DEBUG: No samples pass filters for INV at chr04:3739364-3739487
samplot_vcf - DEBUG: No samples pass filters for INV at chr04:7207168-7207450
samplot_vcf - DEBUG: No samples pass filters for DEL at chr04:13025347-13025378
samplot_vcf - DEBUG: No samples pass filters for INV at chr04:14243953-14244142
samplot_vcf - DEBUG: No samples pass filters for INV at chr04:19011752-19012341
samplot_vcf - DEBUG: No samples pass filters for DEL at chr04:19123520-19123614
samplot_vcf - DEBUG: No samples pass filters for INV at chr04:31612331-31612567
samplot_vcf - DEBUG: Skipping INS at chr04:35236557-35236558, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for DEL at chr04:35238111-35238142
samplot_vcf - DEBUG: No samples pass filters for INV at chr05:1184667-1184862
samplot_vcf - DEBUG: No samples pass filters for INV at chr05:16182224-16187102
samplot_vcf - DEBUG: No samples pass filters for INV at chr05:20851513-20852059
samplot_vcf - DEBUG: No samples pass filters for INV at chr05:21536660-21536869
samplot_vcf - DEBUG: No samples pass filters for INV at chr05:25715440-25717388
samplot_vcf - DEBUG: No samples pass filters for INV at chr05:31012441-31012985
samplot_vcf - DEBUG: No samples pass filters for DEL at chr06:5057162-5057492
samplot_vcf - DEBUG: No samples pass filters for INV at chr06:16108351-16108396
samplot_vcf - DEBUG: Skipping INS at chr06:27979107-27979108, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr06:29832970-29834715
samplot_vcf - DEBUG: No samples pass filters for DEL at chr06:31912692-31912724
samplot_vcf - DEBUG: No samples pass filters for INV at chr06:41073999-41074298
samplot_vcf - DEBUG: No samples pass filters for INV at chr07:18296840-18297148
samplot_vcf - DEBUG: No samples pass filters for DEL at chr07:20317278-20317358
samplot_vcf - DEBUG: No samples pass filters for INV at chr08:2465591-2465843
samplot_vcf - DEBUG: No samples pass filters for INV at chr08:28890626-28890770
samplot_vcf - DEBUG: No samples pass filters for INV at chr08:31386037-31386383
samplot_vcf - DEBUG: No samples pass filters for INV at chr08:33891244-33891478
samplot_vcf - DEBUG: No samples pass filters for INV at chr08:35326629-35326967
samplot_vcf - DEBUG: No samples pass filters for DEL at chr08:35547397-35547471
samplot_vcf - DEBUG: No samples pass filters for DEL at chr08:36492406-36492495
samplot_vcf - DEBUG: No samples pass filters for DEL at chr08:38101551-38101657
samplot_vcf - DEBUG: No samples pass filters for DEL at chr08:38739527-38739978
samplot_vcf - DEBUG: Skipping INS at chr08:42949677-42949678, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr08:44494955-44495178
samplot_vcf - DEBUG: No samples pass filters for INV at chr09:5299344-5299442
samplot_vcf - DEBUG: No samples pass filters for DEL at chr09:15068952-15068985
samplot_vcf - DEBUG: No samples pass filters for INV at chr09:22570476-22572325
samplot_vcf - DEBUG: No samples pass filters for INV at chr09:22812455-22812774
samplot_vcf - DEBUG: No samples pass filters for INV at chr09:26427103-26427325
samplot_vcf - DEBUG: No samples pass filters for DEL at chr09:32621360-32621651
samplot_vcf - DEBUG: Skipping INS at chr09:34107559-34107560, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr09:34622138-34622190
samplot_vcf - DEBUG: Skipping INS at chr09:35739887-35739888, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr10:3853786-3853838
samplot_vcf - DEBUG: No samples pass filters for INV at chr10:9114145-9122345
samplot_vcf - DEBUG: No samples pass filters for INV at chr10:9573190-9573376
samplot_vcf - DEBUG: No samples pass filters for INV at chr10:10005116-10005268
samplot_vcf - DEBUG: No samples pass filters for DEL at chr11:10597249-10597297
samplot_vcf - DEBUG: No samples pass filters for INV at chr11:13166414-13166485
samplot_vcf - DEBUG: Skipping INS at chr11:29967234-29967235, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr11:33441334-33441706
samplot_vcf - DEBUG: No samples pass filters for INV at chr12:3842067-3842330
samplot_vcf - DEBUG: No samples pass filters for DUP at chr12:7601298-17575736
samplot_vcf - DEBUG: No samples pass filters for DEL at chr12:13662332-13662364
samplot_vcf - DEBUG: No samples pass filters for DEL at chr12:18985732-18985769
samplot_vcf - DEBUG: No samples pass filters for INV at chr12:21777686-21777887
samplot_vcf - DEBUG: No samples pass filters for INV at chr12:23886725-23888460
samplot_vcf - DEBUG: No samples pass filters for INV at chr12:34741122-34741542
samplot_vcf - DEBUG: No samples pass filters for INV at chr12:35753138-35753515
samplot_vcf - DEBUG: No samples pass filters for INV at chr12:39753844-39754492
samplot_vcf - DEBUG: No samples pass filters for DEL at chr13:538431-538478
samplot_vcf - DEBUG: No samples pass filters for INV at chr13:1030222-1033562
samplot_vcf - DEBUG: No samples pass filters for INV at chr13:3532095-3532403
samplot_vcf - DEBUG: No samples pass filters for INV at chr13:10034080-10034123
samplot_vcf - DEBUG: No samples pass filters for DEL at chr13:14235473-14235519
samplot_vcf - DEBUG: No samples pass filters for INV at chr13:15571193-15572715
samplot_vcf - DEBUG: Skipping INS at chr13:21625256-21625257, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for DEL at chr14:337036-337086
samplot_vcf - DEBUG: No samples pass filters for DEL at chr14:8056786-8056862
samplot_vcf - DEBUG: Skipping INS at chr14:12914562-12914764, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr14:20197126-20197493
samplot_vcf - DEBUG: No samples pass filters for INV at chr14:25063166-25066631
samplot_vcf - DEBUG: No samples pass filters for DEL at chr14:26070346-26070389
samplot_vcf - DEBUG: No samples pass filters for INV at chr14:31306720-31306785
samplot_vcf - DEBUG: No samples pass filters for INV at chr14:31413225-31413493
samplot_vcf - DEBUG: No samples pass filters for INV at chr15:2926055-2926094
samplot_vcf - DEBUG: No samples pass filters for INV at chr15:12574155-12574355
samplot_vcf - DEBUG: No samples pass filters for INV at chr15:20022599-20022795
samplot_vcf - DEBUG: No samples pass filters for INV at chr15:24493076-24495680
samplot_vcf - DEBUG: No samples pass filters for INV at chr15:28088991-28089163
samplot_vcf - DEBUG: No samples pass filters for INV at chr15:31207904-31208054
samplot_vcf - DEBUG: No samples pass filters for INV at chr15:39543154-39543346
samplot_vcf - DEBUG: No samples pass filters for INV at chr15:44632918-44633176
samplot_vcf - DEBUG: No samples pass filters for INV at chr15:44755793-44755902
samplot_vcf - DEBUG: No samples pass filters for INV at chr16:16077245-16078666
samplot_vcf - DEBUG: No samples pass filters for INV at chr16:24359491-24359566
samplot_vcf - DEBUG: No samples pass filters for DEL at chr16:25917221-25917274
samplot_vcf - DEBUG: No samples pass filters for INV at chr16:27447019-27447094
samplot_vcf - DEBUG: No samples pass filters for DEL at chr16:48248957-48248991
samplot_vcf - DEBUG: No samples pass filters for INV at chr17:2031454-2031756
samplot_vcf - DEBUG: Skipping INS at chr17:2773673-2773674, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for DEL at chr17:9469538-9469585
samplot_vcf - DEBUG: No samples pass filters for INV at chr17:11772041-11772180
samplot_vcf - DEBUG: No samples pass filters for DEL at chr17:19529964-19530044
samplot_vcf - DEBUG: No samples pass filters for DEL at chr17:23968412-23968518
samplot_vcf - DEBUG: No samples pass filters for INV at chr17:24461410-24461447
samplot_vcf - DEBUG: No samples pass filters for INV at chr17:28241194-28243205
samplot_vcf - DEBUG: Skipping INS at chr17:30389343-30389344, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for DEL at chr18:1683333-1683378
samplot_vcf - DEBUG: No samples pass filters for INV at chr18:13094095-13094231
samplot_vcf - DEBUG: No samples pass filters for INV at chr18:13264440-13264542
samplot_vcf - DEBUG: Skipping INS at chr18:15356837-15356838, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr18:17772637-17772900
samplot_vcf - DEBUG: No samples pass filters for INV at chr18:19172989-19174876
samplot_vcf - DEBUG: No samples pass filters for INV at chr18:25128274-25133007
samplot_vcf - DEBUG: No samples pass filters for DEL at chr18:25189390-25189444
samplot_vcf - DEBUG: No samples pass filters for INV at chr18:25985024-25986478
samplot_vcf - DEBUG: No samples pass filters for INV at chr18:26198783-26201634
samplot_vcf - DEBUG: No samples pass filters for DEL at chr18:28920556-28920588
samplot_vcf - DEBUG: No samples pass filters for INV at chr18:30755360-30755758
samplot_vcf - DEBUG: No samples pass filters for INV at chr19:2234616-2234780
samplot_vcf - DEBUG: No samples pass filters for INV at chr19:16770680-16771068
samplot_vcf - DEBUG: No samples pass filters for DEL at chr19:17838820-17838857
samplot_vcf - DEBUG: No samples pass filters for DEL at chr19:21943017-21943052
samplot_vcf - DEBUG: No samples pass filters for INV at chr19:28550430-28554901
samplot_vcf - DEBUG: No samples pass filters for INV at chr19:31582634-31582740
samplot_vcf - DEBUG: No samples pass filters for INV at chr19:36377344-36377376
samplot_vcf - DEBUG: No samples pass filters for INV at chr19:36414737-36414869
samplot_vcf - DEBUG: No samples pass filters for DUP at chr19:39437063-39437112
samplot_vcf - DEBUG: Skipping INS at chr19:42502241-42502242, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr19:44105599-44105889
samplot_vcf - DEBUG: No samples pass filters for INV at chr19:45177024-45177100
samplot_vcf - DEBUG: No samples pass filters for DEL at chr20:9454890-9454931
samplot_vcf - DEBUG: No samples pass filters for INV at chr20:10447059-10447190
samplot_vcf - DEBUG: Skipping INS at chr20:15425960-15425962, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for DEL at chr20:16049281-16049318
samplot_vcf - DEBUG: No samples pass filters for DUP at chr20:23129732-23142776
samplot_vcf - DEBUG: No samples pass filters for DEL at chr20:23129948-23143082
samplot_vcf - DEBUG: No samples pass filters for INV at chr20:29898533-29898865
samplot_vcf - DEBUG: No samples pass filters for DUP at chr20:34059520-34059552
samplot_vcf - DEBUG: No samples pass filters for DEL at chr20:36150319-36150405
samplot_vcf - DEBUG: No samples pass filters for INV at chr20:41509913-41511933
samplot_vcf - DEBUG: Skipping INS at chr21:2533092-2533093, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr21:2623892-2624001
samplot_vcf - DEBUG: No samples pass filters for DEL at chr21:2882640-2882672
samplot_vcf - DEBUG: No samples pass filters for INV at chr21:3234751-3236836
samplot_vcf - DEBUG: Skipping INS at chr21:5065791-5065792, INS type not supported
samplot_vcf - DEBUG: Skipping INS at chr21:19011676-19011677, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr21:23399622-23399904
samplot_vcf - DEBUG: No samples pass filters for DUP at chr21:29145097-29145139
samplot_vcf - DEBUG: No samples pass filters for INV at chr21:36921324-36921569
samplot_vcf - DEBUG: No samples pass filters for INV at chr22:1336213-1336375
samplot_vcf - DEBUG: No samples pass filters for INV at chr22:14202037-14202588
samplot_vcf - DEBUG: No samples pass filters for INV at chr22:23593263-23593314
samplot_vcf - DEBUG: No samples pass filters for INV at chr23:3026113-3026388
samplot_vcf - DEBUG: Skipping INS at chr23:4671483-4671484, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr23:14444905-14447362
samplot_vcf - DEBUG: No samples pass filters for DEL at chr23:17210327-17210433
samplot_vcf - DEBUG: No samples pass filters for DEL at chr23:17319503-17320209
samplot_vcf - DEBUG: No samples pass filters for INV at chr23:18020252-18020553
samplot_vcf - DEBUG: No samples pass filters for DEL at chr23:27116797-27117471
samplot_vcf - DEBUG: No samples pass filters for INV at chr23:29137169-29137210
samplot_vcf - DEBUG: No samples pass filters for DEL at chr23:31074954-31074991
samplot_vcf - DEBUG: No samples pass filters for INV at chr23:32984394-32984586
samplot_vcf - DEBUG: No samples pass filters for INV at chr23:34139724-34141832
samplot_vcf - DEBUG: No samples pass filters for INV at chr23:38506700-38506902
samplot_vcf - DEBUG: No samples pass filters for INV at chr23:41593254-41593412
samplot_vcf - DEBUG: No samples pass filters for DEL at chr24:1912678-1912709
samplot_vcf - DEBUG: No samples pass filters for INV at chr24:6229975-6230281
samplot_vcf - DEBUG: No samples pass filters for INV at chr24:11732822-11733706
samplot_vcf - DEBUG: No samples pass filters for INV at chr24:15459177-15459374
samplot_vcf - DEBUG: No samples pass filters for DEL at chr24:22033965-22034120
samplot_vcf - DEBUG: No samples pass filters for INV at chr24:25423874-25424080
samplot_vcf - DEBUG: No samples pass filters for INV at chr24:30765759-30765843
samplot_vcf - DEBUG: Skipping INS at chr25:12255430-12255431, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr25:13269212-13273961
samplot_vcf - DEBUG: No samples pass filters for INV at chr25:15512963-15514166
samplot_vcf - DEBUG: No samples pass filters for INV at chr25:18973503-18973818
samplot_vcf - DEBUG: No samples pass filters for DUP at chr25:23874594-23874640
samplot_vcf - DEBUG: No samples pass filters for INV at chr26:238868-238921
samplot_vcf - DEBUG: Skipping DEL at chr26:730753-730772, variant length shorter than min_bp
samplot_vcf - DEBUG: No samples pass filters for INV at chr26:6074121-6074518
samplot_vcf - DEBUG: No samples pass filters for DEL at chr26:11763745-11763777
samplot_vcf - DEBUG: No samples pass filters for INV at chr26:15896036-15896249
samplot_vcf - DEBUG: No samples pass filters for INV at chr26:17984275-17984503
samplot_vcf - DEBUG: No samples pass filters for INV at chr26:20009106-20009144
samplot_vcf - DEBUG: No samples pass filters for INV at chr26:25651586-25651658
samplot_vcf - DEBUG: No samples pass filters for INV at chr26:25835039-25835280
samplot_vcf - DEBUG: No samples pass filters for INV at chr26:28748365-28748431
samplot_vcf - DEBUG: No samples pass filters for INV at chr26:33179610-33179643
samplot_vcf - DEBUG: No samples pass filters for DEL at chr26:39169654-39171286
samplot_vcf - DEBUG: No samples pass filters for DEL at chr26:44514812-44514874
samplot_vcf - DEBUG: No samples pass filters for DEL at chr26:44813722-44814002
samplot_vcf - DEBUG: No samples pass filters for INV at chr26:46099213-46099370
samplot_vcf - DEBUG: No samples pass filters for DUP at chr27:38674-38744
samplot_vcf - DEBUG: No samples pass filters for INV at chr27:3722602-3722910
samplot_vcf - DEBUG: Skipping INS at chr27:10309266-10309267, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr27:17935185-17940034
samplot_vcf - DEBUG: No samples pass filters for DEL at chr27:24586535-24586573
samplot_vcf - DEBUG: No samples pass filters for DEL at chr27:24859306-24863343
samplot_vcf - DEBUG: No samples pass filters for INV at chr27:24918982-25444317
samplot_vcf - DEBUG: No samples pass filters for DEL at chr27:25254392-25254441
samplot_vcf - DEBUG: Skipping INS at chr27:25416095-25416130, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr27:25833267-25833399
samplot_vcf - DEBUG: No samples pass filters for DUP at chr27:31836849-31836903
samplot_vcf - DEBUG: No samples pass filters for INV at chr27:40576253-40576431
samplot_vcf - DEBUG: No samples pass filters for DUP at chr28:211875-219731
samplot_vcf - DEBUG: Skipping INS at chr28:422804-422805, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr28:10917386-10917646
samplot_vcf - DEBUG: No samples pass filters for INV at chr28:25140288-25140885
samplot_vcf - DEBUG: No samples pass filters for DUP at chr28:28213515-28215071
samplot_vcf - DEBUG: No samples pass filters for INV at chr28:40611171-40611507
samplot_vcf - DEBUG: No samples pass filters for INV at chr29:1693278-2368038
samplot_vcf - DEBUG: No samples pass filters for DEL at chr29:2145011-2145047
samplot_vcf - DEBUG: Skipping INS at chr29:2400493-2400494, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr29:6892911-6893231
samplot_vcf - DEBUG: No samples pass filters for INV at chr29:23281968-23284329
samplot_vcf - DEBUG: Skipping INS at chr29:25627336-25627337, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for DEL at chr29:39940494-39940770
samplot_vcf - DEBUG: No samples pass filters for INV at chr30:9666878-9666991
samplot_vcf - DEBUG: No samples pass filters for INV at chr30:15621581-15621740
samplot_vcf - DEBUG: No samples pass filters for DEL at chr30:22536212-22536604
samplot_vcf - DEBUG: Skipping INS at chr30:30365000-30365001, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr30:30694743-30694995
samplot_vcf - DEBUG: No samples pass filters for DEL at chr30:36091805-36091836
samplot_vcf - DEBUG: No samples pass filters for INV at chr30:37893281-39321794
samplot_vcf - DEBUG: Skipping INS at chr30:38146401-38146402, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for DEL at chr31:6556444-6557303
samplot_vcf - DEBUG: No samples pass filters for INV at chr31:23330481-23330707
samplot_vcf - DEBUG: No samples pass filters for INV at chr31:28165291-28165454
samplot_vcf - DEBUG: No samples pass filters for INV at chr31:44810297-44810466
samplot_vcf - DEBUG: No samples pass filters for INV at chr32:2121095-2121254
samplot_vcf - DEBUG: No samples pass filters for INV at chr32:10703892-10714479
samplot_vcf - DEBUG: No samples pass filters for DUP at chr32:15161881-15161930
samplot_vcf - DEBUG: No samples pass filters for DEL at chr32:23157592-23157631
samplot_vcf - DEBUG: No samples pass filters for INV at chr33:4018290-4018426
samplot_vcf - DEBUG: No samples pass filters for DEL at chr33:8892956-8893062
samplot_vcf - DEBUG: No samples pass filters for INV at chr33:19218422-19218565
samplot_vcf - DEBUG: Skipping INS at chr33:20556647-20556648, INS type not supported
samplot_vcf - DEBUG: No samples pass filters for INV at chr33:21469524-21469592
samplot_vcf - DEBUG: No samples pass filters for INV at chr33:22338990-22340149
samplot_vcf - DEBUG: No samples pass filters for INV at chr33:22614283-22614520
samplot_vcf - DEBUG: No samples pass filters for INV at chr33:23578195-23578331
samplot_vcf - DEBUG: No samples pass filters for INV at chr33:28347140-28347509
samplot_vcf - DEBUG: VCF entry count: 289
samplot_vcf - DEBUG: VCF entrys filtered out: 257
samplot_vcf - DEBUG:  - No plottable samples: 224
samplot_vcf - DEBUG:  - Skipped: 33