Using gff file with merfin ?
Opened this issue · 3 comments
Hello,
I polished my assembly using arrow and I have a .gff file, but no .vcf.
Is it possible to run Merfin using a .gff file ?
Otherwise do you know a way to cenvert .ggf to .vcf ?
Thanks
Hello @aureliendejode , I think there should be a way to convert your arrow's .gff to .vcf.
Let me take a look at this. Feel free to share your .gff (or part of it) if you have it handy.
Thanks!
Arang
Hello,
Here is a part of the .gff file. Thanks for your help.
##gff-version 3
##pacbio-variant-version 2.1
##date Fri Jul 16 16:48:15 2021
##feature-ontology http://song.cvs.sourceforge.net/*checkout*/song/ontology/sofa.obo?revision=1.12
##source GenomicConsensus 2.3.3
##source-commandline /sw/bioinfo/SMRT/7.0.1/rackham/install/smrtlink-release_7.0.1.66975/bundles/smrttools/install/smrttools-release_7.0.1.66768/private/pacbio/pythonpkgs/GenomicC
onsensus/binwrap/../../../../../private/pacbio/pythonpkgs/GenomicConsensus/bin/variantCaller --skipUnrecognizedContigs -x 5 -q 20 -X120 -v -j 20 --algorithm=arrow -r /proj/snic202
0-6-155/canu_new_pacbio_all_third_lib-6-155/purge_dup/canu_purged.fa -o saxa.canu.10.gff -o saxa.canu.10.fastq -o saxa.canu.10.fasta saxa.canu.chunk9.xml
##source-alignment-file /crex/proj/snic2020-6-155/canu_new_pacbio_all_third_lib-6-155/arrow_grid_on_grid/My_installation/saxa.canu.chunk9.xml
##source-reference-file /proj/snic2020-6-155/canu_new_pacbio_all_third_lib-6-155/purge_dup/canu_purged.fa
##sequence-region tig00000029_1 1 230969
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##sequence-region tig00022667_1 1 2690
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##sequence-region tig00022806_1 1 6118
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##sequence-region tig00022838_1 1 7778
##sequence-region tig00022862_1 1 12765
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##sequence-region tig00022975_1 1 13025
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##sequence-region tig00023561_1 1 28367
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##sequence-region tig00023659_1 1 5582
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##sequence-region tig00023793_1 1 4167
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##sequence-region tig00023943_1 1 6540
##sequence-region tig00024000_1 1 13149
##sequence-region tig00024075_1 1 18057
##sequence-region tig00024093_1 1 2245
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##sequence-region tig00024383_1 1 23161
##sequence-region tig00024474_1 1 15177
##sequence-region tig00024587_1 1 3933
##sequence-region tig00024619_1 1 16690
##sequence-region tig00024623_1 1 9089
##sequence-region tig00024753_1 1 14964
##sequence-region tig00024870_1 1 9194
##sequence-region tig00024927_1 1 13498
##sequence-region tig00024942_1 1 18379
##sequence-region tig00024987_1 1 1240
##sequence-region tig00025027_1 1 5153
##sequence-region tig00025193_1 1 15895
##sequence-region tig00025236_1 1 87343
##sequence-region tig00025350_1 1 6959
##sequence-region tig00025403_1 1 26723
##sequence-region tig00025426_1 1 5265
##sequence-region tig00025440_1 1 5739
##sequence-region tig00025510_1 1 19392
##sequence-region tig00025615_1 1 9519
##sequence-region tig00025632_1 1 12090
##sequence-region tig00025804_1 1 16425
##sequence-region tig00026068_1 1 12604
##sequence-region tig00026120_1 1 1811
##sequence-region tig00026496_1 1 4395
##sequence-region tig00026768_1 1 2744
##sequence-region tig00026869_1 1 10261
##sequence-region tig00026904_1 1 2089
##sequence-region tig00026974_1 1 11459
##sequence-region tig00027034_1 1 8946
##sequence-region tig00027067_1 1 12126
##sequence-region tig00027388_1 1 8026
##sequence-region tig00027456_1 1 3005
##sequence-region tig00059793_1 1 867813
##sequence-region tig00059802_1 1 21202
##sequence-region tig00059822_1 1 77504
##sequence-region tig00059833_1 1 27194
##sequence-region tig00059899_1 1 43530
##sequence-region tig00059927_1 1 54758
##sequence-region tig00059988_1 1 682827
##sequence-region tig00060057_1 1 1532017
##sequence-region tig00060071_1 1 926759
##sequence-region tig00060130_1 1 499427
##sequence-region tig00060143_1 1 64172
##sequence-region tig00060151_1 1 353758
##sequence-region tig00060211_1 1 83671
##sequence-region tig00060220_1 1 11254
##sequence-region tig00060221_1 1 1697
##sequence-region tig00060285_1 1 1767871
##sequence-region tig00060294_1 1 757178
##sequence-region tig00060337_1 1 340016
##sequence-region tig00060377_1 1 526983
##sequence-region tig00060384_1 1 413057
##sequence-region tig00060442_1 1 119291
##sequence-region tig00060472_1 1 377183
##sequence-region tig00060475_1 1 69424
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##sequence-region tig00060514_1 1 953316
##sequence-region tig00060559_1 1 16392
##sequence-region tig00060573_1 1 12204
##sequence-region tig00060591_1 1 15188
##sequence-region tig00060595_1 1 93290
##sequence-region tig00060676_1 1 320227
##sequence-region tig00060697_1 1 68834
##sequence-region tig00060709_1 1 324696
##sequence-region tig00060713_1 1 25047
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##sequence-region tig00060826_1 1 84925
##sequence-region tig00060891_1 1 506298
##sequence-region tig00060922_1 1 109779
##sequence-region tig00060938_1 1 311695
##sequence-region tig00060939_1 1 16934
##sequence-region tig00061059_1 1 370327
##sequence-region tig00061105_1 1 261706
##sequence-region tig00061111_1 1 90166
##sequence-region tig00061119_1 1 335304
##sequence-region tig00061127_1 1 103182
##sequence-region tig00061136_1 1 436477
##sequence-region tig00061190_1 1 10949
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##sequence-region tig00061216_1 1 41596
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##sequence-region tig00061252_1 1 1291364
##sequence-region tig00061278_1 1 10844
##sequence-region tig00061281_1 1 384452
##sequence-region tig00061282_1 1 616785
##sequence-region tig00061313_1 1 186661
##sequence-region tig00061322_1 1 13067
##sequence-region tig00061365_1 1 166807
##sequence-region tig00061371_1 1 370552
##sequence-region tig00061372_1 1 389596
##sequence-region tig00061379_1 1 16003
##sequence-region tig00061415_1 1 26472
##sequence-region tig00061424_1 1 359523
##sequence-region tig00061467_1 1 119351
##sequence-region tig00061479_1 1 387467
##sequence-region tig00061497_1 1 559700
##sequence-region tig00061526_1 1 477702
##sequence-region tig00061565_1 1 132505
##sequence-region tig00061583_1 1 66214
##sequence-region tig00061596_1 1 716763
##sequence-region tig00061597_1 1 272139
##sequence-region tig00061657_1 1 79201
##sequence-region tig00061690_1 1 67573
##sequence-region tig00061704_1 1 559075
##sequence-region tig00061774_1 1 52161
##sequence-region tig00061775_1 1 240366
##sequence-region tig00061812_1 1 98442
##sequence-region tig00061883_1 1 14006
##sequence-region tig00061924_1 1 43738
##sequence-region tig00061937_1 1 398516
##sequence-region tig00061982_1 1 136887
##sequence-region tig00061983_1 1 6554
##sequence-region tig00062016_1 1 839470
##sequence-region tig00062073_1 1 154645
##sequence-region tig00062094_1 1 397271
##sequence-region tig00062100_1 1 449949
##sequence-region tig00062158_1 1 64961
##sequence-region tig00062160_1 1 14130
##sequence-region tig00062186_1 1 4732
##sequence-region tig00062234_1 1 588200
##sequence-region tig00062251_1 1 404312
##sequence-region tig00062316_1 1 264995
##sequence-region tig00062451_1 1 487053
##sequence-region tig00062456_1 1 190301
##sequence-region tig00062498_1 1 171976
##sequence-region tig00062537_1 1 121017
##sequence-region tig00062640_1 1 96556
##sequence-region tig00062731_1 1 257810
##sequence-region tig00062744_1 1 92068
##sequence-region tig00062764_1 1 305466
##sequence-region tig00062811_1 1 218120
##sequence-region tig00062842_1 1 28722
##sequence-region tig00062849_1 1 15787
##sequence-region tig00062850_1 1 286560
##sequence-region tig00062879_1 1 99827
##sequence-region tig00062915_1 1 129421
##sequence-region tig00063048_1 1 206144
##sequence-region tig00063133_1 1 11046
##sequence-region tig00063138_1 1 519761
##sequence-region tig00063225_1 1 110871
##sequence-region tig00063234_1 1 297553
##sequence-region tig00063353_1 1 6741
##sequence-region tig00063355_1 1 31659
##sequence-region tig00063359_1 1 67498
##sequence-region tig00063396_1 1 156202
##sequence-region tig00063417_1 1 44452
##sequence-region tig00063475_1 1 178126
##sequence-region tig00063485_1 1 20346
##sequence-region tig00063492_1 1 447279
##sequence-region tig00063513_1 1 122833
##sequence-region tig00063526_1 1 9927
##sequence-region tig00063608_1 1 122118
##sequence-region tig00063776_1 1 19700
##sequence-region tig00063785_1 1 316465
##sequence-region tig00063786_1 1 13618
##sequence-region tig00063803_1 1 88685
##sequence-region tig00063869_1 1 71087
##sequence-region tig00063905_1 1 252346
##sequence-region tig00063922_1 1 11838
##sequence-region tig00063929_1 1 228211
##sequence-region tig00063933_1 1 62242
##sequence-region tig00063940_1 1 15842
##sequence-region tig00063972_1 1 127213
##sequence-region tig00064054_1 1 120880
##sequence-region tig00064119_1 1 11346
##sequence-region tig00064138_1 1 112107
##sequence-region tig00064173_1 1 13763
##sequence-region tig00064208_1 1 183932
##sequence-region tig00064297_1 1 58536
##sequence-region tig00064304_1 1 220806
##sequence-region tig00064307_1 1 231567
##sequence-region tig00064331_1 1 188138
##sequence-region tig00064394_1 1 10249
##sequence-region tig00064429_1 1 75508
##sequence-region tig00064442_1 1 376725
##sequence-region tig00064453_1 1 24118
##sequence-region tig00064462_1 1 35767
##sequence-region tig00064491_1 1 21769
##sequence-region tig00064552_1 1 12574
##sequence-region tig00064667_1 1 24457
##sequence-region tig00064674_1 1 28170
##sequence-region tig00064784_1 1 40993
##sequence-region tig00065023_1 1 80728
##sequence-region tig00065134_1 1 141218
##sequence-region tig00065145_1 1 158074
##sequence-region tig00065200_1 1 176710
##sequence-region tig00065250_1 1 81054
##sequence-region tig00065256_1 1 56206
##sequence-region tig00065272_1 1 13299
##sequence-region tig00065327_1 1 111574
##sequence-region tig00065372_1 1 51251
##sequence-region tig00065393_1 1 100187
##sequence-region tig00065431_1 1 57872
##sequence-region tig00065445_1 1 30315
##sequence-region tig00065462_1 1 13981
##sequence-region tig00065478_1 1 226464
##sequence-region tig00065512_1 1 146889
##sequence-region tig00065534_1 1 73486
##sequence-region tig00065554_1 1 107634
##sequence-region tig00065576_1 1 116058
##sequence-region tig00065636_1 1 38408
##sequence-region tig00065637_1 1 5945
##sequence-region tig00065639_1 1 8470
##sequence-region tig00065658_1 1 116853
##sequence-region tig00065684_1 1 141071
##sequence-region tig00065719_1 1 30613
##sequence-region tig00065721_1 1 1881
##sequence-region tig00065731_1 1 33275
##sequence-region tig00065798_1 1 63615
##sequence-region tig00065886_1 1 5784
##sequence-region tig00065956_1 1 72695
##sequence-region tig00065992_1 1 3584
##sequence-region tig00066054_1 1 8653
##sequence-region tig00066182_1 1 23832
##sequence-region tig00066217_1 1 43350
##sequence-region tig00066220_1 1 7932
##sequence-region tig00066235_1 1 9429
##sequence-region tig00066247_1 1 40903
##sequence-region tig00066262_1 1 2531
##sequence-region tig00066264_1 1 10430
##sequence-region tig00066267_1 1 15516
##sequence-region tig00066307_1 1 4454
##sequence-region tig00066322_1 1 20495
##sequence-region tig00066378_1 1 14170
##sequence-region tig00066409_1 1 11934
##sequence-region tig00066442_1 1 12444
##sequence-region tig00066518_1 1 22190
##sequence-region tig00066556_1 1 11994
##sequence-region tig00066652_1 1 10659
##sequence-region tig00066663_1 1 12223
##sequence-region tig00066730_1 1 2939
##sequence-region tig00066876_1 1 2309
##sequence-region tig00066887_1 1 2016
##sequence-region tig00066929_1 1 17226
##sequence-region tig00066941_1 1 1657
##sequence-region tig00066952_1 1 1269
##sequence-region tig00066957_1 1 10105
##sequence-region tig00067010_1 1 1942
##sequence-region tig00067017_1 1 9310
##sequence-region tig00067023_1 1 3070
##sequence-region tig00067055_1 1 3244
##sequence-region tig00067078_1 1 8180
tig00000029_1 . insertion 262 262 . . . reference=.;variantSeq=C;coverage=26;confidence=93
tig00000029_1 . deletion 429 429 . . . reference=T;variantSeq=.;coverage=27;confidence=43
tig00000029_1 . insertion 451 451 . . . reference=.;variantSeq=T;coverage=27;confidence=33
tig00000029_1 . insertion 1193 1193 . . . reference=.;variantSeq=G;coverage=31;confidence=88
tig00000029_1 . insertion 1921 1921 . . . reference=.;variantSeq=GAGAGA;coverage=53;confidence=93
tig00000029_1 . insertion 2759 2759 . . . reference=.;variantSeq=A;coverage=56;confidence=93
tig00000029_1 . insertion 2950 2950 . . . reference=.;variantSeq=T;coverage=58;confidence=83
tig00000029_1 . substitution 3480 3480 . . . reference=A;variantSeq=G;coverage=51;confidence=93
tig00000029_1 . substitution 3615 3615 . . . reference=T;variantSeq=A;coverage=52;confidence=93
tig00000029_1 . insertion 4280 4280 . . . reference=.;variantSeq=CA;coverage=55;confidence=93
tig00000029_1 . deletion 5636 5636 . . . reference=A;variantSeq=.;coverage=54;confidence=93
tig00000029_1 . substitution 5640 5640 . . . reference=G;variantSeq=A;coverage=55;confidence=93
tig00000029_1 . insertion 6294 6294 . . . reference=.;variantSeq=CCC;coverage=50;confidence=20
tig00000029_1 . deletion 12134 12135 . . . reference=AC;variantSeq=.;coverage=89;confidence=93
tig00000029_1 . substitution 14603 14603 . . . reference=G;variantSeq=C;coverage=50;confidence=93
tig00000029_1 . insertion 14615 14615 . . . reference=.;variantSeq=AGAGAGAGAGAGAGAGAG;coverage=49;confidence=93
tig00000029_1 . insertion 16475 16475 . . . reference=.;variantSeq=GT;coverage=66;confidence=93
tig00000029_1 . insertion 17757 17757 . . . reference=.;variantSeq=AC;coverage=68;confidence=93
tig00000029_1 . insertion 17860 17860 . . . reference=.;variantSeq=CACA;coverage=68;confidence=93
tig00000029_1 . insertion 18758 18758 . . . reference=.;variantSeq=AC;coverage=56;confidence=93
tig00000029_1 . insertion 20146 20146 . . . reference=.;variantSeq=G;coverage=65;confidence=93
tig00000029_1 . deletion 20511 20512 . . . reference=GT;variantSeq=.;coverage=54;confidence=93
tig00000029_1 . insertion 20847 20847 . . . reference=.;variantSeq=CCC;coverage=47;confidence=22
tig00000029_1 . deletion 20882 20882 . . . reference=C;variantSeq=.;coverage=46;confidence=27
tig00000029_1 . insertion 21207 21207 . . . reference=.;variantSeq=T;coverage=47;confidence=93
tig00000029_1 . insertion 21509 21509 . . . reference=.;variantSeq=GTGT;coverage=47;confidence=93
tig00000029_1 . insertion 21768 21768 . . . reference=.;variantSeq=C;coverage=48;confidence=93
tig00000029_1 . insertion 21912 21912 . . . reference=.;variantSeq=A;coverage=45;confidence=93
tig00000029_1 . insertion 22570 22570 . . . reference=.;variantSeq=GA;coverage=49;confidence=93
tig00000029_1 . insertion 24233 24233 . . . reference=.;variantSeq=A;coverage=93;confidence=93
tig00000029_1 . substitution 24244 24244 . . . reference=C;variantSeq=A;coverage=95;confidence=93
tig00000029_1 . substitution 24257 24257 . . . reference=C;variantSeq=A;coverage=95;confidence=71
tig00000029_1 . insertion 28373 28373 . . . reference=.;variantSeq=A;coverage=50;confidence=93
tig00000029_1 . insertion 29173 29173 . . . reference=.;variantSeq=TCTC;coverage=81;confidence=93
tig00000029_1 . insertion 29454 29454 . . . reference=.;variantSeq=CTTTC;coverage=67;confidence=80
tig00000029_1 . insertion 29455 29455 . . . reference=.;variantSeq=C;coverage=67;confidence=93
tig00000029_1 . insertion 29583 29583 . . . reference=.;variantSeq=TC;coverage=70;confidence=93
tig00000029_1 . deletion 29842 29842 . . . reference=T;variantSeq=.;coverage=78;confidence=93
tig00000029_1 . substitution 29843 29843 . . . reference=C;variantSeq=A;coverage=78;confidence=93
tig00000029_1 . insertion 30717 30717 . . . reference=.;variantSeq=A;coverage=92;confidence=93
tig00000029_1 . insertion 31268 31268 . . . reference=.;variantSeq=C;coverage=106;confidence=78
tig00000029_1 . insertion 38980 38980 . . . reference=.;variantSeq=G;coverage=112;confidence=68
tig00000029_1 . insertion 39094 39094 . . . reference=.;variantSeq=AGAG;coverage=104;confidence=93
tig00000029_1 . insertion 51531 51531 . . . reference=.;variantSeq=CTCT;coverage=109;confidence=93
tig00000029_1 . insertion 51624 51624 . . . reference=.;variantSeq=CT;coverage=110;confidence=93
tig00000029_1 . insertion 53531 53531 . . . reference=.;variantSeq=C;coverage=106;confidence=71
tig00000029_1 . insertion 56259 56259 . . . reference=.;variantSeq=G;coverage=87;confidence=20
tig00000029_1 . insertion 56295 56295 . . . reference=.;variantSeq=C;coverage=89;confidence=52
tig00000029_1 . insertion 56354 56354 . . . reference=.;variantSeq=TG;coverage=91;confidence=93
tig00000029_1 . insertion 56652 56652 . . . reference=.;variantSeq=A;coverage=101;confidence=21
tig00000029_1 . insertion 56816 56816 . . . reference=.;variantSeq=CA;coverage=103;confidence=93
tig00000029_1 . insertion 57748 57748 . . . reference=.;variantSeq=GA;coverage=99;confidence=93
tig00000029_1 . insertion 63114 63114 . . . reference=.;variantSeq=ACACAC;coverage=92;confidence=93
Hello Arang,
I am in the final steps of the assembly for my genome before scaffolding and I'd really like to get going with merfin.
Any news about this ?
Thanks for your help