VCF output returns a TSV file

nvnieuwk commented 1 year ago

Hi,

I'm trying to run the tool with the -vcf 1 option, but am getting TSV files as output instead of VCF files. Am I doing something wrong or is this feature not fully implemented yet?

Command:

AnnotSV \
    -annotationsDir AnnotSV \
    -outputFile test.vcf \
    -SVinputFile sv_query.vcf.gz \
    -vcf 1

Output folder:

├── 20230403_AnnotSV
├── AnnotSV -> /home/nvnieuwk/Documents/data/AnnotSV/share/AnnotSV
├── sv_query.vcf.gz -> /tmp/tmp8i_0jtyz/stage-b63e3e39-fa0c-456c-b890-5684c6f7b0c2/33/9f416cecabdc1793bb044e8cec64bd/sv_query.vcf.gz
├── sv_query.vcf.gz.tbi -> /tmp/tmp8i_0jtyz/stage-b63e3e39-fa0c-456c-b890-5684c6f7b0c2/27/9c146bee77905d49f0f78b47066e00/sv_query.vcf.gz.tbi
├── test.vcf.tsv
├── test.vcf.unannotated.tsv
└── test.vcf.variantconvert.log

Variantconvert log:

python3 /tmp/AnnotSV-3.3.2/share/python3/variantconvert/variantconvert convert -i 20230403_AnnotSV/test.vcf.tsv -o 20230403_AnnotSV/test.vcf.vcf -fi annotsv -fo vcf -c /tmp/AnnotSV-3.3.2/share/python3/variantconvert/configs/GRCh38/annotsv3_from_vcf.json

2023-04-03 13:29:16 [INFO] running variantconvert 1.2.2
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/opt/conda/lib/python3.8/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/tmp/AnnotSV-3.3.2/share/python3/variantconvert/variantconvert/__main__.py", line 226, in <module>
    main()
  File "/tmp/AnnotSV-3.3.2/share/python3/variantconvert/variantconvert/__main__.py", line 209, in main
    main_convert(args)
  File "/tmp/AnnotSV-3.3.2/share/python3/variantconvert/variantconvert/__main__.py", line 74, in main_convert
    converter.convert(args.inputFile, args.outputFile)
  File "/tmp/AnnotSV-3.3.2/share/python3/variantconvert/variantconvert/converters/vcf_from_annotsv.py", line 460, in convert
    self.sample_list = self._get_sample_list()
  File "/tmp/AnnotSV-3.3.2/share/python3/variantconvert/variantconvert/converters/vcf_from_annotsv.py", line 76, in _get_sample_list
    raise ValueError(
ValueError: 0      When using an AnnotSV file generated from a VC...
1      When using an AnnotSV file generated from a VC...
2      When using an AnnotSV file generated from a VC...
3      When using an AnnotSV file generated from a VC...
4      When using an AnnotSV file generated from a VC...
                             ...                        
475    When using an AnnotSV file generated from a VC...
476    When using an AnnotSV file generated from a VC...
477    When using an AnnotSV file generated from a VC...
478    When using an AnnotSV file generated from a VC...
479    When using an AnnotSV file generated from a VC...
Name: Samples_ID, Length: 480, dtype: object

Thanks in advance -Nicolas

lgmgeo commented 1 year ago

Hi,

Everything in your command line looks correct. Normally AnnotSV returns a TSV file and variantconvert returns a VCF file. As shown in test.vcf.variantconvert.log, you have a bug with the variantconvert tool. May I ask you to duplicate your bug report in https://github.com/SamuelNicaise/variantconvert/issues ?

Best,

Véronique

nvnieuwk commented 1 year ago

Thanks @lgmgeo I will repost the issue there

lgmgeo commented 1 year ago

cf https://github.com/SamuelNicaise/variantconvert/issues/22

lgmgeo commented 1 year ago

Sorry, I did not notice that you used: -outputFile test.vcf

Just to let you know, you need to run AnnotSV with: -outputFile test.annotated.tsv

The test.annotated.tsv file will be created by AnnotSV. Then, with the -vcf 1 option, this TSV file will be converted to VCF by variantconvert (test.annotated.vcf). test.annotated.variantconvert.log will be the variantconvert log file.

But I don't think that could explain the error message in the variantconvert log.

nvnieuwk commented 1 year ago

Thank you for the tip, it didn't fix the error indeed but I'll keep that in mind for future runs!

lgmgeo commented 1 year ago

Just a few questions...

Did you set the -SVinputInfo option to 1 in AnnotSV?
In your input file (sv_query.vcf.gz), do you have a classic header with sample names? Is the GT defined for variants?
Can you share the AnnotSV output header (test.vcf.tsv)?

nvnieuwk commented 1 year ago

Hi, The VCF file looks like this (it's publicly available on https://github.com/nf-core/test-datasets/tree/modules/data/genomics/homo_sapiens/illumina/vcf):

##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##source=MergeVCF
##SVDB_version=2.4.0 cmd="/usr/local/bin/svdb --merge --priority tiddit,cnvnator,manta --same_order --vcf /home/ramprasad.neethiraj/analysis/rare_disease_test/justhusky/analysis_gatk_samtoolsdev/justhusky/sv_combinevariantcallsets/justhusky_manta.vcf:manta /home/ramprasad.neethiraj/analysis/rare_disease_test/justhusky/analysis_gatk_samtoolsdev/justhusky/sv_combinevariantcallsets/justhusky_cnvnator_ar.vcf:cnvnator /home/ramprasad.neethiraj/analysis/rare_disease_test/justhusky/analysis_gatk_samtoolsdev/justhusky/sv_combinevariantcallsets/justhusky_tiddit.vcf:tiddit"
##ALT=<ID=BND,Description="Break end">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=DUP:TANDEM,Description="Tandem Duplication">
##ALT=<ID=INS,Description="Insertion">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=TDUP,Description="Tandem duplication">
##INFO=<ID=BND_DEPTH,Number=1,Type=Integer,Description="Read depth at local translocation breakend">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END">
##INFO=<ID=CIGAR,Number=A,Type=String,Description="CIGAR alignment for each alternate indel allele">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS">
##INFO=<ID=COVA,Number=1,Type=Float,Description="Coverage on window A">
##INFO=<ID=COVB,Number=1,Type=Float,Description="Coverage on window B">
##INFO=<ID=COVM,Number=1,Type=Float,Description="The coverage between A and B">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical homology at event breakpoints">
##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical homology at event breakpoints">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=JUNCTION_QUAL,Number=1,Type=Integer,Description="If the SV junction is part of an EVENT (ie. a multi-adjacency variant), this field provides the QUAL value for the adjacency in question only">
##INFO=<ID=LEFT_SVINSSEQ,Number=.,Type=String,Description="Known left side of insertion for an insertion of unknown length">
##INFO=<ID=LFA,Number=1,Type=Integer,Description="Links from window A">
##INFO=<ID=LFB,Number=1,Type=Integer,Description="Links from window B">
##INFO=<ID=LTE,Number=1,Type=Integer,Description="Links to event">
##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakend">
##INFO=<ID=MATE_BND_DEPTH,Number=1,Type=Integer,Description="Read depth at remote translocation mate breakend">
##INFO=<ID=OR,Number=4,Type=Integer,Description="Orientation of the pairs (FF,RR,RF,FR)">
##INFO=<ID=ORSR,Number=2,Type=Integer,Description="Orientation of the split reads (inverted,normal)">
##INFO=<ID=QUALA,Number=1,Type=Float,Description="The average mapping quality of the reads in window A">
##INFO=<ID=QUALB,Number=1,Type=Float,Description="The average mapping quality of the reads in window B">
##INFO=<ID=RIGHT_SVINSSEQ,Number=.,Type=String,Description="Known right side of insertion for an insertion of unknown length">
##INFO=<ID=SAMPLES,Number=.,Type=String,Description="Sample genotyped to have the variant">
##INFO=<ID=SVINSLEN,Number=.,Type=Integer,Description="Length of insertion">
##INFO=<ID=SVINSSEQ,Number=.,Type=String,Description="Sequence of insertion">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=natorP1,Number=1,Type=Float,Description="e-val by t-test">
##INFO=<ID=natorP2,Number=1,Type=Float,Description="e-val by Gaussian tail">
##INFO=<ID=natorP3,Number=1,Type=Float,Description="e-val by t-test (middle)">
##INFO=<ID=natorP4,Number=1,Type=Float,Description="e-val by Gaussian tail (middle)">
##INFO=<ID=natorPE,Number=1,Type=Integer,Description="Number of paired-ends support the event">
##INFO=<ID=natorQ0,Number=1,Type=Float,Description="Fraction of reads with 0 mapping quality">
##INFO=<ID=natorRD,Number=1,Type=Float,Description="Normalized RD">
##contig=<ID=chr22,length=50818468>
#CHROM  POS ID  REF QUAL    FILTER  INFO    test1   test2   test3
chr22   1   CNVnator_del_1  N   <DEL>   .   PASS    END=16050000;SVTYPE=DEL;SVLEN=-16050000;IMPRECISE;natorRD=0;natorP1=9.92975e-15;natorP2=0;natorP3=9.93099e-15;natorP4=0;natorQ0=-1;set=cnvnator GT:CN   1/1:0   1/1:0   1/1:0
chr22   16096001    CNVnator_dup_2  A   <DUP>   .   PASS    END=16280000;SVTYPE=DUP;SVLEN=184000;IMPRECISE;natorRD=2.15564;natorP1=0;natorP2=2.87091e+09;natorP3=0;natorP4=2.87091e+09;natorQ0=0.464156;set=cnvnator    GT:CN   ./.:.   1/1:2   1/1:2
chr22   16101001    CNVnator_dup_2  A   <DUP>   .   PASS    END=16147000;SVTYPE=DUP;SVLEN=46000;IMPRECISE;natorRD=1.77343;natorP1=1.40109e-08;natorP2=2.3055e+07;natorP3=2.18558e-08;natorP4=2.84357e+07;natorQ0=0.491164;set=cnvnator  GT:CN   1/1:2   ./.:.   ./.:.
chr22   16122937    MantaDEL:153392:1:1:0:0:0   AGTGCCACCGGAGGTGTAAGGAGCTGTTTCCCATTCAGATGGAGGGTGTCAAGCTCACAGTCAACAAAGGGTTGAGTAACCGTTTCCAGGTGAACCACACAGTAGCCCTCAGCGCAATCGGGGAGTCCAACTACCACTTCGGGGTCACGTATGTGGGGACAAAGCAGCTGAGTCCCACAGAGG ACACGTACA   386 MaxDepth    END=16123119;SVTYPE=DEL;SVLEN=-182;CIGAR=1M8I182D;set=filterInmanta GT:FT:GQ:PL:PR:SR   0/1:PASS:310:360,0,999:48,7:93,14   0/1:PASS:75:125,0,999:53,9:124,10   0/0:HomRef:247:0,197,999:61,3:140,5
chr22   16160001    CNVnator_dup_3  C   <DUP>   .   PASS    END=16240000;SVTYPE=DUP;SVLEN=80000;IMPRECISE;natorRD=1.7461;natorP1=0;natorP2=2.19812e+09;natorP3=0;natorP4=2.21285e+09;natorQ0=0.417885;set=cnvnator  GT:CN   0/1:2   ./.:.   ./.:.
chr22   16173001    CNVnator_dup_3  G   <DUP>   .   PASS    END=16260000;SVTYPE=DUP;SVLEN=87000;IMPRECISE;natorRD=2.04111;natorP1=0;natorP2=1.17483e-08;natorP3=0;natorP4=2.94917e-08;natorQ0=0.403095;set=cnvnator GT:CN   ./.:.   ./.:.   1/1:2
chr22   16246618    MantaDEL:196548:0:0:0:0:0   CGCTCAAAGAGCAACCAGCCACCTCTGCAAGGTCTGGCCAGGGCTACAGAAGGCCCCCCTGGATGGTAATCCTGGCTGCGTTCTGCACCTGAACATAAAGTCCTCCTCAAGATGGCCTGTGGTCTGCCTCTAGGCAACCAAGAAGCCCGCAGTGCTACACGACCCCTGAGGCATGGACTAGAGCCCCAAAGGCAATGCACAACCTGCTCCTGAGCCTGCTGCTCGTTTCCTCTCTGTGGCTACATTTGTAGCAGAGTAGTTGCACTGAGCTGTGTGCACGCCAGGCAAAGCCAGGCTG  C   92  PASS    END=16246915;SVTYPE=DEL;SVLEN=-297;CIGAR=1M297D;CIPOS=0,31;HOMLEN=31;HOMSEQ=GCTCAAAGAGCAACCAGCCACCTCTGCAAGG;set=manta   GT:FT:GQ:PL:PR:SR   0/0:HomRef:222:0,172,999:39,0:64,1  0/1:PASS:92:142,0,987:55,8:69,7 0/0:HomRef:176:0,126,999:61,4:90,3
chr22   16262001    CNVnator_dup_4  G   <DUP>   .   PASS    END=16280000;SVTYPE=DUP;SVLEN=18000;IMPRECISE;natorRD=2.28248;natorP1=0.0354184;natorP2=1.02409e-26;natorP3=0.356319;natorP4=8.89141e-23;natorQ0=0.515424;set=cnvnator  GT:CN   ./.:.   ./.:.   ./1:2
chr22   16282001    CNVnator_dup_4;CNVnator_dup_3;CNVnator_dup_5    A   <DUP>   .   PASS    END=16341000;SVTYPE=DUP;SVLEN=59000;IMPRECISE;natorRD=1.8248;natorP1=0;natorP2=3.13177e+06;natorP3=0;natorP4=3.94644e+06;natorQ0=0.481623;set=cnvnator  GT:CN   1/1:2   1/1:2   1/1:2
chr22   16344001    CNVnator_dup_6  A   <DUP>   .   PASS    END=16395000;SVTYPE=DUP;SVLEN=51000;IMPRECISE;natorRD=1.74569;natorP1=0;natorP2=0.0223828;natorP3=0;natorP4=0.0610276;natorQ0=0.364383;set=cnvnator GT:CN   ./.:.   ./.:.   0/1:2
chr22   16359001    CNVnator_dup_4  T   <DUP>   .   PASS    END=16455000;SVTYPE=DUP;SVLEN=96000;IMPRECISE;natorRD=1.95544;natorP1=0;natorP2=9.17991e-40;natorP3=0;natorP4=9.40059e-39;natorQ0=0.489137;set=cnvnator GT:CN   ./.:.   1/1:2   ./.:.
chr22   16360001    CNVnator_dup_5  A   <DUP>   .   PASS    END=16390000;SVTYPE=DUP;SVLEN=30000;IMPRECISE;natorRD=1.7426;natorP1=5.96421e-06;natorP2=7.59428e-26;natorP3=5.42308e-05;natorP4=1.5334e-23;natorQ0=0.386764;set=cnvnator   GT:CN   0/1:2   ./.:.   ./.:.
chr22   16393001    CNVnator_dup_6  A   <DUP>   .   PASS    END=16455000;SVTYPE=DUP;SVLEN=62000;IMPRECISE;natorRD=1.58015;natorP1=0;natorP2=0.808477;natorP3=0;natorP4=1.6434;natorQ0=0.488955;set=cnvnator GT:CN   0/1:2   ./.:.   ./.:.
chr22   16396001    CNVnator_dup_7  G   <DUP>   .   PASS    END=16430000;SVTYPE=DUP;SVLEN=34000;IMPRECISE;natorRD=1.9537;natorP1=1.0677e-07;natorP2=4.5805e-19;natorP3=5.06426e-07;natorP4=1.97714e-17;natorQ0=0.467298;set=cnvnator    GT:CN   ./.:.   ./.:.   1/1:2
chr22   16432001    CNVnator_dup_8  C   <DUP>   .   PASS    END=16458000;SVTYPE=DUP;SVLEN=26000;IMPRECISE;natorRD=1.74138;natorP1=7.76733e-07;natorP2=9.74759e-25;natorP3=1.4317e-06;natorP4=9.52995e-41;natorQ0=0.519278;set=cnvnator  GT:CN   ./.:.   ./.:.   0/1:2
chr22   16560088    MantaDEL:196585:0:0:0:0:0   TAGCAGTGTTCTGGATTCCTATGTAGGGGAGAAACACTCAGAACCCAACAGCAGTGTTCTGGAATCCTTTGTGATGGACATACATTC T   400 MaxMQ0Frac  END=16560174;SVTYPE=DEL;SVLEN=-86;CIGAR=1M86D;CIPOS=0,2;HOMLEN=2;HOMSEQ=AG;set=filterInmanta    GT:FT:GQ:PL:PR:SR   0/1:PASS:187:353,0,184:1,0:14,18    0/1:PASS:97:147,0,441:6,0:29,7  0/0:HomRef:155:0,105,700:5,0:36,0
chr22   16698001    CNVnator_del_7;CNVnator_del_5;CNVnator_del_9    N   <DEL>   .   PASS    END=16848000;SVTYPE=DEL;SVLEN=-150000;IMPRECISE;natorRD=0.00140091;natorP1=1.06248e-12;natorP2=0;natorP3=1.07684e-12;natorP4=0;natorQ0=0.672414;set=cnvnator    GT:CN   1/1:0   1/1:0   1/1:0
chr22   16847851    SV_23088_1  N   ]hs37d5:4001530]N   0   Ploidy  SVTYPE=BND;CIPOS=0,382;CIEND=-57,0;COVA=28.1964;COVB=0;LFA=44;LFB=12;LTE=12;OR=0,0,6,0;ORSR=0,6;QUALA=55;QUALB=0;set=filterIntiddit GT:CN:DV:RV:DR:RR   1/1:.:6:6:2,0:3,0   1/1:.:10:4:3,0:7,0  1/1:.:13:5:0,0:2,0
chr22   16847851    SV_23115_1  N   ]hs37d5:11720938]N  0   Ploidy  SVTYPE=BND;CIPOS=0,203;CIEND=-275,0;COVA=29.5802;COVB=0;LFA=41;LFB=24;LTE=22;OR=0,0,22,0;ORSR=0,0;QUALA=52;QUALB=0;set=filterIntiddit   GT:CN:DV:RV:DR:RR   1/1:.:22:0:2,0:3,0  ./.:.:.:.:.:.   ./.:.:.:.:.:.
chr22   16847851    SV_23116_1  N   [hs37d5:17909719[N  0   Ploidy  SVTYPE=BND;CIPOS=0,173;CIEND=0,2;COVA=29.6486;COVB=0;LFA=40;LFB=8;LTE=8;OR=0,2,0,0;ORSR=6,0;QUALA=51;QUALB=0;set=filterIntiddit GT:CN:DV:RV:DR:RR   1/1:.:2:6:2,0:3,0   1/1:.:8:2:3,0:7,0   ./.:.:.:.:.:.
chr22   16851756    MantaDEL:196606:0:0:0:0:0   CATCGAATGGAATTGAATGGAATTATCATCGAATGGACTCGAATGGAATTATCATCGAATGGACTCA CG  999 PASS    END=16851822;SVTYPE=DEL;SVLEN=-66;CIGAR=1M1I66D;set=manta   GT:FT:GQ:PL:PR:SR   1/1:PASS:62:999,65,0:0,0:0,25   0/1:PASS:205:328,0,201:5,0:14,9 0/0:HomRef:128:0,78,517:7,0:29,0
chr22   16853424    MantaINS:24149:1:1:1:0:0    TT  TCGAATGGAATCATCAAATAGCATCAAATGGAATCATCATCGAATGAAATC 999 PASS    END=16853425;SVTYPE=INS;SVLEN=50;CIGAR=1M50I1D;set=manta    GT:FT:GQ:PL:PR:SR   1/1:PASS:56:913,59,0:0,0:0,20   0/1:PASS:89:492,0,86:1,0:7,14   0/0:HomRef:92:0,42,280:2,0:16,0
chr22   16858544    SV_23089_1  N   N[hs37d5:9392054[   0   Ploidy  SVTYPE=BND;CIPOS=-101,0;CIEND=0,66;COVA=41.5207;COVB=0;LFA=7;LFB=6;LTE=6;OR=0,0,0,0;ORSR=0,6;QUALA=52;QUALB=0;set=filterIntiddit    GT:CN:DV:RV:DR:RR   1/1:.:0:6:44,0:35,0 ./.:.:.:.:.:.   ./.:.:.:.:.:.
chr22   16867661    MantaDEL:7:364344:364344:0:0:1  GCGACTTTTTTCCTGCCGCGGCTTTTTACCCCCTGCCGCCGTGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCCCCACCCCGCCTC  GT  81  SampleFT    END=16867750;SVTYPE=DEL;SVLEN=-89;CIGAR=1M1I89D;set=filterInmanta   GT:FT:GQ:PL:PR:SR   1/1:MinGQ:4:81,5,0:0,0:0,3  1/1:MinGQ:6:103,7,0:2,0:5,5 0/0:HomRef:48:0,0,0:4,0:0,0
chr22   16882598    SV_23090_1  N   N]hs37d5:19967263]  0   Ploidy  SVTYPE=BND;CIPOS=-165,0;CIEND=-126,0;COVA=62.0674;COVB=0;LFA=10;LFB=9;LTE=9;OR=9,0,0,0;ORSR=0,0;QUALA=34;QUALB=0;set=filterIntiddit GT:CN:DV:RV:DR:RR   1/1:.:9:0:49,0:38,0 1/1:.:14:0:58,0:35,0    ./.:.:.:.:.:.
chr22   16907604    SV_23091_1  N   [hs37d5:23918161[N  0   Ploidy  SVTYPE=BND;CIPOS=0,112;CIEND=0,170;COVA=58.2913;COVB=0;LFA=8;LFB=11;LTE=7;OR=0,7,0,0;ORSR=0,0;QUALA=46;QUALB=0;set=filterIntiddit   GT:CN:DV:RV:DR:RR   1/1:.:7:0:45,0:33,0 1/1:.:10:0:51,0:44,0    ./.:.:.:.:.:.
chr22   16918013    MantaINS:16361:2:2:0:10:0   C   <INS>   999 MaxDepth    END=16918013;SVTYPE=INS;CIPOS=0,10;CIEND=0,10;HOMLEN=10;HOMSEQ=AAAAATTTGC;LEFT_SVINSSEQ=AAAAATTTGCGAGTGCTCAATGGTGCCCAGGCTGGAGTGCAGTGGCGTGATCTCAGCTCGCT;RIGHT_SVINSSEQ=AGAAATCGGATGGTTGCCGTGTCTGTGTAGAAAGAAGTATACATGGGAGACTTTTCATTTTGTTCTGTACTAAGAAAAATTCTTCTGCCTTGGGATCCTGTTGATCTGTGACCTTATCCCCAACCCTGTGCTCTCTGAAACATGTGCTGTGTCCACTCAGGGTTAAATGGATTAAGGACGGTGCAAGATGTGCTTTGTTAAAAAGATGCTTGAAGGCAGCATGCTCGTTAAGAGTCATCACCACTCCCTAATCTCAAGTACCCAGGGACACAAACACGGCGGAAGGCCGCAAGGTCCTCTGCCTAGGAAAACCAGAGACCTTTGTTCACTTGTTTATCTGCTGACCTTCCCTCCACTATTGTCCTATGACCCTGCCAAATCCCCCTCTGCGAGAAACACCCAAGAATGATCAATAACAAAAAAAAAAAAAGAAAAA;set=filterInmanta    GT:FT:GQ:PL:PR:SR   0/1:PASS:400:966,0,397:26,7:29,30   0/1:PASS:533:596,0,530:28,3:23,22   0/1:PASS:458:717,0,455:22,8:25,19
chr22   16926142    SV_23392_1  N   N[hs37d5:28914695[  0   Ploidy  SVTYPE=BND;CIPOS=-241,0;CIEND=0,127;COVA=70.9931;COVB=0;LFA=8;LFB=6;LTE=6;OR=0,0,0,6;ORSR=0,0;QUALA=41;QUALB=0;set=filterIntiddit   GT:CN:DV:RV:DR:RR   ./.:.:.:.:.:.   ./.:.:.:.:.:.   1/1:.:6:0:66,0:43,0
chr22   16937816    SV_23092_1  N   N[hs37d5:28925790[  0   Ploidy  SVTYPE=BND;CIPOS=-258,0;CIEND=0,257;COVA=54.0756;COVB=0;LFA=11;LFB=13;LTE=11;OR=0,0,0,11;ORSR=0,0;QUALA=39;QUALB=0;set=filterIntiddit   GT:CN:DV:RV:DR:RR   1/1:.:11:0:41,0:20,0    1/1:.:28:0:55,0:28,0    1/1:.:9:0:35,0:10,0
chr22   16945693    SV_23093_1  N   ]hs37d5:28934017]N  0   Ploidy  SVTYPE=BND;CIPOS=0,269;CIEND=-422,0;COVA=48.1626;COVB=0;LFA=27;LFB=35;LTE=27;OR=0,0,18,9;ORSR=0,0;QUALA=42;QUALB=0;set=filterIntiddit   GT:CN:DV:RV:DR:RR   1/1:.:27:0:47,0:31,0    1/1:.:40:0:44,0:31,0    1/1:.:39:0:46,0:38,0
chr22   16962001    CNVnator_del_6;CNVnator_del_10  C   <DEL>   .   PASS    END=16984000;SVTYPE=DEL;SVLEN=-22000;IMPRECISE;natorRD=0.43394;natorP1=7.24421e-12;natorP2=0;natorP3=7.96863e-12;natorP4=0;natorQ0=0.651507;set=cnvnator    GT:CN   ./.:.   0/1:1   0/1:1
chr22   16965001    CNVnator_del_8  T   <DEL>   .   PASS    END=16984000;SVTYPE=DEL;SVLEN=-19000;IMPRECISE;natorRD=0.511174;natorP1=1.26273e-07;natorP2=4.37866e-24;natorP3=3.68464e-06;natorP4=1.24661e-20;natorQ0=0.611277;set=cnvnator   GT:CN   0/1:1   ./.:.   ./.:.
chr22   16989001    CNVnator_del_9  G   <DEL>   .   PASS    END=17005000;SVTYPE=DEL;SVLEN=-16000;IMPRECISE;natorRD=0.546664;natorP1=1.16644e-05;natorP2=7.4211e-13;natorP3=2.44592e-05;natorP4=6.27383e-24;natorQ0=0.858621;set=cnvnator    GT:CN   0/1:1   ./.:.   ./.:.
chr22   16990001    CNVnator_del_7  A   <DEL>   .   PASS    END=17005000;SVTYPE=DEL;SVLEN=-15000;IMPRECISE;natorRD=0.485471;natorP1=7.42963e-07;natorP2=1.15053e-33;natorP3=3.58544e-06;natorP4=4.91365e-41;natorQ0=0.89847;set=cnvnator    GT:CN   ./.:.   0/1:1   ./.:.
chr22   17015285    SV_23094_1  N   [hs37d5:17907698[N  0   Ploidy  SVTYPE=BND;CIPOS=0,465;CIEND=0,116;COVA=20.3165;COVB=0;LFA=19;LFB=11;LTE=9;OR=0,9,0,0;ORSR=0,0;QUALA=53;QUALB=0;set=filterIntiddit  GT:CN:DV:RV:DR:RR   1/1:.:9:0:14,0:18,0 1/1:.:16:0:5,0:14,0 1/1:.:19:0:12,0:22,0
chr22   17015347    SV_23117_1  N   N]hs37d5:17909751]  0   Ploidy  SVTYPE=BND;CIPOS=-277,0;CIEND=-257,0;COVA=22.4524;COVB=0;LFA=17;LFB=24;LTE=12;OR=12,0,0,0;ORSR=0,0;QUALA=53;QUALB=0;set=filterIntiddit  GT:CN:DV:RV:DR:RR   1/1:.:12:0:12,0:17,0    1/1:.:14:1:7,0:16,0 1/1:.:12:0:11,0:19,0
chr22   17027001    CNVnator_del_10 C   <DEL>   .   PASS    END=17029000;SVTYPE=DEL;SVLEN=-2000;IMPRECISE;natorRD=0.384708;natorP1=40951.4;natorP2=0.00154432;natorP3=1;natorP4=1;natorQ0=0.239286;set=cnvnator GT:CN   0/1:1   ./.:.   ./.:.
chr22   17040858    MantaDEL:7:364355:364355:12:1:0 AAGCCAGCCAAGCCAGACAACCAGCCAAGCCAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCCAGTCAAGCCAGCCATCCAGCCAAGCTAGCCAAGCCAGGAAAGCTACCCAGCCAGCCAAGCCATCCAGCCACCCAGCCAGCCAGGCCAGCC    A   57  PASS    END=17041021;SVTYPE=DEL;SVLEN=-163;CIGAR=1M163D;CIPOS=0,5;HOMLEN=5;HOMSEQ=AGCCA;set=manta   GT:FT:GQ:PL:PR:SR   0/1:PASS:51:107,0,49:10,0:7,5   0/0:HomRef:56:0,6,39:7,3:6,3    0/0:HomRef:68:0,18,112:12,1:17,0
chr22   17048832    SV_23095_1  N   N]hs37d5:5262305]   0   Ploidy  SVTYPE=BND;CIPOS=-224,0;CIEND=-252,0;COVA=29.6663;COVB=0;LFA=17;LFB=13;LTE=10;OR=10,0,0,0;ORSR=0,0;QUALA=41;QUALB=0;set=filterIntiddit  GT:CN:DV:RV:DR:RR   1/1:.:10:0:30,0:29,0    1/1:.:9:0:20,0:15,0 1/1:.:10:0:27,0:20,0
chr22   17157001    CNVnator_del_8;CNVnator_del_11  A   <DEL>   .   PASS    END=17196000;SVTYPE=DEL;SVLEN=-39000;IMPRECISE;natorRD=0.354149;natorP1=4.08647e-12;natorP2=0;natorP3=4.30737e-12;natorP4=0;natorQ0=0.697634;set=cnvnator   GT:CN   ./.:.   0/1:1   0/1:1
chr22   17163001    CNVnator_del_11 A   <DEL>   .   PASS    END=17177000;SVTYPE=DEL;SVLEN=-14000;IMPRECISE;natorRD=0.357582;natorP1=0.00089766;natorP2=2.7022e-10;natorP3=0.018009;natorP4=1.41176e-07;natorQ0=0.746212;set=cnvnator    GT:CN   0/1:1   ./.:.   ./.:.
chr22   17180001    CNVnator_del_12 G   <DEL>   .   PASS    END=17196000;SVTYPE=DEL;SVLEN=-16000;IMPRECISE;natorRD=0.340894;natorP1=9.36911e-08;natorP2=0;natorP3=6.18699e-06;natorP4=0;natorQ0=0.831489;set=cnvnator   GT:CN   0/1:1   ./.:.   ./.:.
chr22   17240001    CNVnator_del_13;CNVnator_del_9;CNVnator_del_12  G   <DEL>   .   PASS    END=17278000;SVTYPE=DEL;SVLEN=-38000;IMPRECISE;natorRD=0.278026;natorP1=4.19401e-12;natorP2=0;natorP3=4.42701e-12;natorP4=0;natorQ0=0.839726;set=cnvnator   GT:CN   0/1:1   0/1:1   0/1:1
chr22   17370708    MantaDEL:168359:0:0:0:0:0   TTAGCTACTATTTGCTGAGCATCTGTCAAGTCTGTCTGTAGCATGGAAGATCTGAGTACAGGGGAAACTGGATTAGTAACAGTGGGTCAGAAAATTATATAATATTCAACCAAAATTCCTGCTTTACATACACAGCACCTGGTATTTCCAGAACTAGAAGGTAAAGAAATTATTTGTGCTTGAACTTGCAGAAAACTGCCTTTTCCCTTCTTCTCTTGCATCTTAACCTGGAGCTTCCCTTTTCTTGAGCCTCAGTGTGCTTCCCAACTCAATTTATAATTGACTTCCTGCAGTTTCTCCTTAGGACAGGGCTTTGTTTTGGGGGTGGTTAATTTGTAGGGTTCA   T   999 PASS    END=17371052;SVTYPE=DEL;SVLEN=-344;CIGAR=1M344D;CIPOS=0,3;HOMLEN=3;HOMSEQ=TAG;set=manta GT:FT:GQ:PL:PR:SR   0/1:PASS:452:502,0,844:42,0:58,16   0/1:PASS:509:559,0,946:53,0:61,17   0/1:PASS:346:396,0,534:32,0:33,13
chr22   17500832    SV_23096_1  N   N]hs37d5:19616605]  0   Ploidy  SVTYPE=BND;CIPOS=0,0;CIEND=-335,0;COVA=38.9861;COVB=0;LFA=10;LFB=73;LTE=8;OR=7,0,0,0;ORSR=1,0;QUALA=43;QUALB=0;set=filterIntiddit   GT:CN:DV:RV:DR:RR   1/1:.:7:1:32,0:20,0 ./.:.:.:.:.:.   ./.:.:.:.:.:.
chr22   17665782    MantaDEL:196645:0:0:0:0:0   ACACTCTAGCCTGGGTGACAGAGGTGGAGGCTGTAGTGAGCTGTCATCACACCACCG   A   497 PASS    END=17665838;SVTYPE=DEL;SVLEN=-56;CIGAR=1M56D;CIPOS=0,22;HOMLEN=22;HOMSEQ=CACTCTAGCCTGGGTGACAGAG;set=manta  GT:FT:GQ:PL:PR:SR   1/1:PASS:15:294,18,0:0,0:4,9    1/1:MinGQ:12:214,15,0:0,0:0,8   1/1:MinGQ:7:147,9,0:0,0:0,5
chr22   17770001    CNVnator_del_14 A   <DEL>   .   PASS    END=17779000;SVTYPE=DEL;SVLEN=-9000;IMPRECISE;natorRD=0.062738;natorP1=0.00141224;natorP2=0;natorP3=0.00216166;natorP4=0;natorQ0=0.10061;set=cnvnator   GT:CN   1/1:0   ./.:.   ./.:.
chr22   17770352    SV_22999_1:tiddit|MantaDEL:196642:0:1:0:0:0:manta   N   <DEL>   99  PASS    SVTYPE=DEL;CIPOS=-290,0;CIEND=0,401;END=17779109;SVLEN=8758;COVM=0.332503;COVA=23.2664;COVB=28.5034;LFA=40;LFB=36;LTE=36;OR=0,0,0,24;ORSR=0,12;QUALA=49;QUALB=56;SVINSLEN=1;SVINSSEQ=C;VARID=MantaDEL:196642:0:1:0:0:0:manta;set=tiddit-manta   GT:CN:DV:RV:DR:RR   1/1:2:24:12:0,5:0,5 0/1:1:19:8:15,23:11,13  ./.:.:.:.:.:.
chr22   17850265    MantaINS:7:364453:364453:0:6:0  C   <INS>   999 PASS    END=17850266;SVTYPE=INS;LEFT_SVINSSEQ=GGGGGTTGTTGTTGTGGCGCGGGCAGCCCCGCCCCCTCCTCGTGGGCGGCCCCTCCCCCAGGCCCCGCGTCCGGCCCCTCCGCCCCTAGCCCCATCTGTTTCTCCGGCGGGGACTCGATTATATTGTAAGGGACTGGGGGCGGCCGCCGCCGCAGCCGCGGGATGGGGCGAGCGCGCGGACCCCGCGGGCAGCCGCAGCCGCAGCCGCCTCAGTAGTTCGGGCCCCCGCGCCGCCGCCCCCCGCCCGGCGCCCGCCCTCGGCTCCTGCACTCGCCGAGCGGCGGCAGCAGCGGGAGGAGCGCCCCGCCGCCCCCGCCGAGGACCGCGCGGAGGCTGCGGCGCTGCCGCGGCGGGAGTCCCAGGTCGGCGGGCAGAGCGCGGGCAGCGAGGGGCCGCCGCCTGTGCCGCAGCGGGGAGATGTGCCC;RIGHT_SVINSSEQ=CCGGGACTTCTCCGGTGGGCTGGGGCTGGGTGTGGGCGCGAGGGCTGCGCGCGCTCGCCGCCCGGTGCCATTGAGGCGCGAGCCAGCTGCTCCGGCGGGGCCGGGCGCGGGGGG;set=manta GT:FT:GQ:PL:PR:SR   1/1:PASS:91:999,94,0:0,9:0,33   1/1:PASS:46:616,49,0:0,2:0,23   1/1:PASS:58:801,61,0:0,5:0,22
chr22   17863744    MantaINS:67562:1:1:0:0:0    G   GATTACAGACATGCACCACCACGTCTGGCTAATTTTCTTTTTTTTGGATTTTTACT    999 PASS    END=17863744;SVTYPE=INS;SVLEN=55;CIGAR=1M55I;CIPOS=0,2;HOMLEN=2;HOMSEQ=AT;set=manta GT:FT:GQ:PL:PR:SR   1/1:PASS:56:969,59,0:0,0:0,21   1/1:PASS:62:999,65,0:0,0:0,24   1/1:PASS:77:999,80,0:0,0:0,29
chr22   18003607    SV_23301_1  N   <DEL>   2   PASS    SVTYPE=DEL;CIPOS=-275,0;CIEND=0,325;END=18004197;SVLEN=591;COVM=12.7138;COVA=20.1062;COVB=19.199;LFA=15;LFB=13;LTE=8;OR=0,0,0,8;ORSR=0,0;QUALA=45;QUALB=52;set=tiddit   GT:CN:DV:RV:DR:RR   ./.:.:.:.:.:.   ./.:.:.:.:.:.   0/1:1:8:0:16,19:11,22
chr22   18047360    MantaDEL:7:101016:101016:0:0:0  CTATCCTTGCTTTTATTTATTTATTTATTTATTTATTTATTTATTTTATTTTATTTTATTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACCACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCT C   564 PASS    END=18047718;SVTYPE=DEL;SVLEN=-358;CIGAR=1M358D;CIPOS=0,15;HOMLEN=15;HOMSEQ=TATCCTTGCTTTTAT;set=manta   GT:FT:GQ:PL:PR:SR   0/1:PASS:226:425,0,223:21,5:14,11   0/0:HomRef:153:0,103,501:25,0:21,0  0/1:PASS:189:239,0,206:20,10:18,6
chr22   18047377    SV_23000_1  N   N[22:18047719[  21  PASS    SVTYPE=BND;CIPOS=-318,0;CIEND=0,321;COVM=23.2314;COVA=26.2124;COVB=30.6395;LFA=23;LFB=18;LTE=18;OR=0,0,0,8;ORSR=0,10;QUALA=59;QUALB=60;set=tiddit   GT:CN:DV:RV:DR:RR   0/1:.:8:10:24,38:14,22  ./.:.:.:.:.:.   0/1:.:6:6:41,35:25,16
chr22   18057820    SV_23001_1:tiddit|MantaDEL:196683:0:2:0:0:0:manta   N   <DEL>   99  PASS    SVTYPE=DEL;CIPOS=-224,0;CIEND=0,341;END=18060458;SVLEN=2639;COVM=0.587604;COVA=20.6404;COVB=31.3752;LFA=22;LFB=24;LTE=21;OR=0,0,0,21;ORSR=0,0;QUALA=54;QUALB=59;HOMLEN=20;HOMSEQ=ATTCTCCTGCCTCAGCCTCC;VARID=MantaDEL:196683:0:2:0:0:0:manta;set=tiddit-manta    GT:CN:DV:RV:DR:RR   1/1:2:21:0:0,5:0,5  0/1:1:8:0:15,15:10,10   0/1:1:13:1:16,23:12,15
chr22   18099516    MantaDEL:7:282494:282494:0:0:0  GAAAGAGTCATACAAGAGGCCAGGCGCGGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGTGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAA G   999 PASS    END=18099826;SVTYPE=DEL;SVLEN=-310;CIGAR=1M310D;CIPOS=0,16;HOMLEN=16;HOMSEQ=AAAGAGTCATACAAGA;set=manta  GT:FT:GQ:PL:PR:SR   0/1:PASS:150:686,0,147:20,11:25,20  1/1:PASS:57:901,60,0:0,15:0,21  0/1:PASS:163:213,0,172:21,5:18,6
chr22   18099534    SV_23002_1  N   <DEL>   99  PASS    SVTYPE=DEL;CIPOS=-100,0;CIEND=0,1;END=18099827;SVLEN=294;COVM=18.5874;COVA=37.5778;COVB=26.8743;LFA=22;LFB=20;LTE=20;OR=0,0,0,0;ORSR=0,20;QUALA=60;QUALB=55;set=tiddit  GT:CN:DV:RV:DR:RR   0/1:1:0:20:35,39:17,14  0/1:2:0:20:22,34:4,2    0/1:0:4:6:24,34:13,17
chr22   18283896    MantaDEL:7:95680:95680:0:0:0    ATCCTGAGTTTCCTTTTTCTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCCGGGACTACAGGCGCCCGCCACTACGCCCGGCTAATTTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC A   716 PASS    END=18284218;SVTYPE=DEL;SVLEN=-322;CIGAR=1M322D;CIPOS=0,19;HOMLEN=19;HOMSEQ=TCCTGAGTTTCCTTTTTCT;set=manta   GT:FT:GQ:PL:PR:SR   0/0:HomRef:103:0,53,246:24,0:18,0   0/1:PASS:80:452,0,77:10,9:8,10  0/1:PASS:53:364,0,50:8,6:11,8
chr22   18283917    SV_24246_1  N   <DEL>   24  PASS    SVTYPE=DEL;CIPOS=-19,0;CIEND=0,268;END=18284219;SVLEN=303;COVM=19.8635;COVA=20.5681;COVB=34.0426;LFA=12;LFB=9;LTE=9;OR=0,0,0,1;ORSR=0,8;QUALA=53;QUALB=58;set=tiddit    GT:CN:DV:RV:DR:RR   ./.:.:.:.:.:.   0/1:0:1:8:29,31:13,17   ./.:.:.:.:.:.
chr22   18283917    SV_23305_1  N   N[22:18284219[  4   PASS    SVTYPE=BND;CIPOS=-238,0;CIEND=0,311;COVM=20.6204;COVA=22.4057;COVB=25.0165;LFA=8;LFB=10;LTE=8;OR=0,0,0,2;ORSR=0,6;QUALA=57;QUALB=57;set=tiddit  GT:CN:DV:RV:DR:RR   ./.:.:.:.:.:.   ./.:.:.:.:.:.   0/1:.:2:6:21,25:8,14
chr22   18394639    MantaINS:7:364534:364534:0:0:0  GA  GCTTTGGAATGCCATCAGGAGGAAGCTTAGATGAAAAATGCACTATGGATTACTGAGATTCCC 999 PASS    END=18394640;SVTYPE=INS;SVLEN=62;CIGAR=1M62I1D;set=manta    GT:FT:GQ:PL:PR:SR   0/0:HomRef:125:0,75,498:0,0:25,0    0/1:PASS:130:999,0,127:0,0:14,27    1/1:PASS:107:999,110,0:0,0:0,38
chr22   18466176    MantaDEL:196727:0:0:0:0:0   TCATCTCTACCTATTATCCTCATGACAGAACCCTGTGCGCCCCAAGGATGGAGAC T   410 PASS    END=18466230;SVTYPE=DEL;SVLEN=-54;CIGAR=1M54D;CIPOS=0,55;HOMLEN=55;HOMSEQ=CATCTCTACCTATTATCCTCATGACAGAACCCTGTGCGCCCCAAGGATGGAGACC;set=manta GT:FT:GQ:PL:PR:SR   0/0:HomRef:92:0,42,268:5,0:15,0 0/0:HomRef:79:0,29,170:7,0:20,0 0/1:PASS:49:460,0,46:7,0:16,12
chr22   18481069    SV_24247_1  N   ]22:18481357]N  4   Smear   SVTYPE=BND;CIPOS=0,249;CIEND=-251,0;COVM=27.5949;COVA=28.2591;COVB=27.2074;LFA=28;LFB=12;LTE=7;OR=0,0,0,0;ORSR=0,7;QUALA=59;QUALB=59;set=filterIntiddit GT:CN:DV:RV:DR:RR   ./.:.:.:.:.:.   0/1:.:0:7:35,30:10,21   ./.:.:.:.:.:.
chr22   18588724    MantaDUP:TANDEM:7:364556:364557:0:0:0   G   <DUP:TANDEM>    47  PASS    END=18589376;SVTYPE=DUP;SVLEN=652;IMPRECISE;CIPOS=-259,259;CIEND=-330,330;set=manta GT:FT:GQ:PL:PR  0/1:MinGQ:4:51,0,280:19,7   0/1:PASS:38:88,0,442:30,10  0/1:MinGQ:5:53,0,491:33,9
chr22   18668722    SV_23097_1  N   ]hs37d5:386286]N    0   Ploidy  SVTYPE=BND;CIPOS=0,333;CIEND=-66,0;COVA=29.5601;COVB=0;LFA=8;LFB=10;LTE=8;OR=0,0,8,0;ORSR=0,0;QUALA=46;QUALB=0;set=filterIntiddit   GT:CN:DV:RV:DR:RR   1/1:.:8:0:16,0:16,0 1/1:.:6:0:28,0:30,0 1/1:.:7:0:45,0:39,0
chr22   18711001    CNVnator_del_13 A   <DEL>   .   PASS    END=18713000;SVTYPE=DEL;SVLEN=-2000;IMPRECISE;natorRD=0.438135;natorP1=26058.8;natorP2=0.00445059;natorP3=1;natorP4=1;natorQ0=0.997732;set=cnvnator GT:CN   ./.:.   ./.:.   0/1:1
chr22   18727001    CNVnator_del_10 C   <DEL>   .   PASS    END=18734000;SVTYPE=DEL;SVLEN=-7000;IMPRECISE;natorRD=0.496386;natorP1=15.6275;natorP2=4.95059e-13;natorP3=435.417;natorP4=8.18021e-07;natorQ0=0.490405;set=cnvnator    GT:CN   ./.:.   0/1:1   ./.:.
chr22   18749001    CNVnator_del_15 A   <DEL>   .   PASS    END=18751000;SVTYPE=DEL;SVLEN=-2000;IMPRECISE;natorRD=0.25973;natorP1=6791.63;natorP2=4.76469e-12;natorP3=1;natorP4=1;natorQ0=0.470149;set=cnvnator GT:CN   0/1:1   ./.:.   ./.:.
chr22   18760001    CNVnator_dup_16;CNVnator_dup_11 A   <DUP>   .   PASS    END=18801000;SVTYPE=DUP;SVLEN=41000;IMPRECISE;natorRD=1.94821;natorP1=1.50821e-09;natorP2=1.56315e-20;natorP3=4.21724e-09;natorP4=4.18325e-19;natorQ0=0.392439;set=cnvnator GT:CN   1/1:2   1/1:2   ./.:.
chr22   18765001    CNVnator_dup_14 C   <DUP>   .   PASS    END=18825000;SVTYPE=DUP;SVLEN=60000;IMPRECISE;natorRD=2.39289;natorP1=0;natorP2=14731.9;natorP3=0;natorP4=22109.7;natorQ0=0.442265;set=cnvnator GT:CN   ./.:.   ./.:.   ./1:2
chr22   18829001    CNVnator_dup_17 C   <DUP>   .   PASS    END=18872000;SVTYPE=DUP;SVLEN=43000;IMPRECISE;natorRD=1.95678;natorP1=0;natorP2=2.65365e-08;natorP3=0;natorP4=1.64487e-07;natorQ0=0.332046;set=cnvnator GT:CN   1/1:2   ./.:.   ./.:.
chr22   18831001    CNVnator_dup_12;CNVnator_dup_15 A   <DUP>   .   PASS    END=18855000;SVTYPE=DUP;SVLEN=24000;IMPRECISE;natorRD=1.88894;natorP1=6.86942e-06;natorP2=1.29235e-09;natorP3=8.11597e-05;natorP4=4.36785e-08;natorQ0=0.312255;set=cnvnator GT:CN   ./.:.   1/1:2   ./1:3
chr22   18837349    SV_23003_1  N   ]22:21047653]N  4   PASS    SVTYPE=BND;CIPOS=0,263;CIEND=-523,0;COVM=28.3557;COVA=47.8936;COVB=25.2448;LFA=12;LFB=14;LTE=12;OR=0,0,8,4;ORSR=0,0;QUALA=18;QUALB=53;set=tiddit    GT:CN:DV:RV:DR:RR   0/1:.:12:0:40,51:24,39  0/1:.:10:0:31,25:24,18  ./.:.:.:.:.:.
chr22   18844524    SV_24249_1  N   ]22:24658098]N  1   BelowExpectedLinks  SVTYPE=BND;CIPOS=0,265;CIEND=-27,0;COVM=29.3537;COVA=96.7045;COVB=58.9876;LFA=6;LFB=6;LTE=6;OR=0,0,6,0;ORSR=0,0;QUALA=31;QUALB=44;set=filterIntiddit    GT:CN:DV:RV:DR:RR   ./.:.:.:.:.:.   0/1:.:6:0:95,62:55,43   ./.:.:.:.:.:.
chr22   18863001    CNVnator_dup_13 A   <DUP>   .   PASS    END=18872000;SVTYPE=DUP;SVLEN=9000;IMPRECISE;natorRD=2.13486;natorP1=0.00530322;natorP2=0;natorP3=0.571319;natorP4=0;natorQ0=0.373387;set=cnvnator  GT:CN   ./.:.   1/1:2   ./.:.
chr22   18880642    SV_23087_1  N   [GL000212.1:40471[N 0   Ploidy  SVTYPE=BND;CIPOS=0,205;CIEND=0,272;COVA=65.8603;COVB=0;LFA=20;LFB=13;LTE=6;OR=0,6,0,0;ORSR=0,0;QUALA=26;QUALB=0;set=filterIntiddit  GT:CN:DV:RV:DR:RR   1/1:.:6:0:70,0:49,0 1/1:.:12:0:71,0:42,0    ./.:.:.:.:.:.
chr22   18954948    SV_23004_1  N   <INV>   2   BelowExpectedLinks  SVTYPE=INV;CIPOS=0,190;CIEND=0,235;END=20258837;SVLEN=1303890;COVM=30.2078;COVA=33.5643;COVB=26.1895;LFA=12;LFB=13;LTE=10;OR=6,4,0,0;ORSR=0,0;QUALA=58;QUALB=53;set=filterIntiddit  GT:CN:DV:RV:DR:RR   0/1:.:10:0:46,48:44,33  0/1:.:14:0:47,45:39,31  0/1:.:14:0:56,51:33,33
chr22   18955291    MantaBND:196764:0:1:1:0:0:0:manta|MantaBND:196764:0:1:1:0:0:1:manta T   T]22:20258548]  24  PASS    SVTYPE=BND;MATEID=MantaBND:196764:0:1:1:0:0:1;IMPRECISE;CIPOS=-191,191;BND_DEPTH=121;MATE_BND_DEPTH=110;VARID=MantaBND:196764:0:1:1:0:0:1:manta;set=manta   GT:FT:GQ:PL:PR  0/0:HomRef:81:0,31,686:43,6 0/1:PASS:24:74,0,598:40,10  0/0:HomRef:93:0,43,871:54,7
chr22   18957860    SV_23308_1  N   <INV>   1   PASS    SVTYPE=INV;CIPOS=0,37;CIEND=0,280;END=20255857;SVLEN=1297998;COVM=29.7444;COVA=51.0611;COVB=22.8762;LFA=14;LFB=17;LTE=7;OR=0,7,0,0;ORSR=0,0;QUALA=53;QUALB=60;set=tiddit    GT:CN:DV:RV:DR:RR   ./.:.:.:.:.:.   ./.:.:.:.:.:.   0/1:.:7:0:45,12:37,24
chr22   18977575    MantaDEL:196862:0:0:0:0:0   CTGATCACATTTCAACATGAGATTTGGAGGGGCCAGACCTCAAAACTGCATCAGATACATTCATGT  C   999 PASS    END=18977640;SVTYPE=DEL;SVLEN=-65;CIGAR=1M65D;CIPOS=0,1;HOMLEN=1;HOMSEQ=T;set=manta GT:FT:GQ:PL:PR:SR   0/1:PASS:265:369,0,262:4,0:18,10    0/1:PASS:155:205,0,220:2,0:14,6 1/1:PASS:47:830,50,0:0,0:0,17
chr22   19123752    MantaDEL:196828:0:0:0:0:0   GTAGTCCCAGTTACTTGGGAGGTTGAGGCAGGAGAATCACTTGAACCCAAAAATCAAACTAAATATTCGCCACTATTTTC    G   273 PASS    END=19123831;SVTYPE=DEL;SVLEN=-79;CIGAR=1M79D;CIPOS=0,80;HOMLEN=80;HOMSEQ=TAGTCCCAGTTACTTGGGAGGTTGAGGCAGGAGAATCACTTGAACCCAAAAATCAAACTAAATATTCGCCACTATTTTCT;set=manta    GT:FT:GQ:PL:PR:SR   0/0:HomRef:68:0,18,120:8,0:6,0  1/1:PASS:18:326,21,0:0,0:0,7    0/0:HomRef:70:0,20,264:5,0:16,1
chr22   19155934    MantaDEL:196856:0:0:0:0:0   TCCTGTGCACCTTGGTAAACACACACCTGTCCGTCCAGGTAAATGCCCCACTCACTCA  T   413 PASS    END=19155991;SVTYPE=DEL;SVLEN=-57;CIGAR=1M57D;CIPOS=0,40;HOMLEN=40;HOMSEQ=CCTGTGCACCTTGGTAAACACACACCTGTCCGTCCAGGTA;set=manta    GT:FT:GQ:PL:PR:SR   0/0:HomRef:170:0,120,798:15,0:41,0  0/1:PASS:168:260,0,165:1,0:11,8 0/1:PASS:203:253,0,266:4,0:17,7
chr22   19306696    MantaDEL:196833:0:0:0:0:0   TTTTGATTATTTGGTGTTTATGTAAGAGGTATTAAATTTTCAATTTCAAATTCCAATTGTTCAGTGTTGGT TAAAGTATATAGAAAGTA  248 PASS    END=19306766;SVTYPE=DEL;SVLEN=-70;CIGAR=1M17I70D;set=manta  GT:FT:GQ:PL:PR:SR   0/0:HomRef:128:0,78,502:3,0:29,0    0/0:HomRef:176:0,126,838:10,0:48,0  0/1:PASS:248:298,0,355:5,0:23,10
chr22   19361445    MantaINS:7:364882:364882:0:0:0  C   CTGCTCTGGCTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCATGCCATTCTCCTG 315 PASS    END=19361445;SVTYPE=INS;SVLEN=126;CIGAR=1M126I;CIPOS=0,15;HOMLEN=15;HOMSEQ=TGCTCTGGCTTTTTT;set=manta    GT:FT:GQ:PL:PR:SR   0/1:PASS:108:158,0,175:1,6:12,13    0/0:HomRef:119:0,69,382:3,0:17,0    0/1:PASS:207:257,0,246:0,7:16,6
chr22   19558189    MantaDEL:196799:0:0:0:1:0   GTGGGGTAATGTGGGGTAAGGCTGGGATAAGATAGAGAAAGGTTGGGGTAAAGTTGGAGTAAGGA   G   28  PASS    END=19558253;SVTYPE=DEL;SVLEN=-64;CIGAR=1M64D;CIPOS=0,8;HOMLEN=8;HOMSEQ=TGGGGTAA;set=manta  GT:FT:GQ:PL:PR:SR   0/0:HomRef:35:15,0,40:1,0:3,1   0/1:PASS:28:78,0,41:0,0:6,5 0/0:HomRef:55:0,5,27:0,0:1,2
chr22   19947322    MantaDEL:196835:0:0:0:0:0   TCCCCCATGGCTCTTGGCCGTTGGGGCCCAGTTGGCCGCAGAGCCTTTGGCCTTGAGCACTTCCCCAG    T   999 PASS    END=19947389;SVTYPE=DEL;SVLEN=-67;CIGAR=1M67D;CIPOS=0,18;HOMLEN=18;HOMSEQ=CCCCCATGGCTCTTGGCC;set=manta  GT:FT:GQ:PL:PR:SR   1/1:PASS:56:890,59,0:0,0:0,20   1/1:PASS:71:999,74,0:0,0:0,27   1/1:PASS:65:999,68,0:0,0:0,24

The output header (in test.tsv) looks like this:

AnnotSV_ID  SV_chrom    SV_start    SV_end  SV_length   SV_type Samples_ID  ID  REF QUAL    FILTER  INFO    test1   test2   test3   Annotation_mode CytoBand    Gene_name   Gene_count  Tx  Tx_start    Tx_end  Overlapped_tx_length    Overlapped_CDS_length   Overlapped_CDS_percent  Frameshift  Exon_count  Location    Location2   Dist_nearest_SS Nearest_SS_type Intersect_start Intersect_end   RE_gene P_gain_phen P_gain_hpo  P_gain_source   P_gain_coord    P_loss_phen P_loss_hpo  P_loss_source   P_loss_coord    P_ins_phen  P_ins_hpo   P_ins_source    P_ins_coord po_P_gain_phen  po_P_gain_hpo   po_P_gain_source    po_P_gain_coord po_P_gain_percent   po_P_loss_phen  po_P_loss_hpo   po_P_loss_source    po_P_loss_coord po_P_loss_percent   P_snvindel_nb   P_snvindel_phen B_gain_source   B_gain_coord    B_gain_AFmax    B_loss_source   B_loss_coord    B_loss_AFmax    B_ins_source    B_ins_coord B_ins_AFmax B_inv_source    B_inv_coord B_inv_AFmax po_B_gain_allG_source   po_B_gain_allG_coord    po_B_gain_someG_source  po_B_gain_someG_coord   po_B_loss_allG_source   po_B_loss_allG_coord    po_B_loss_someG_source  po_B_loss_someG_coord   TAD_coordinate  ENCODE_experiment   GC_content_left GC_content_right    Repeat_coord_left   Repeat_type_left    Repeat_coord_right  Repeat_type_right   Gap_left    Gap_right   SegDup_left SegDup_right    ENCODE_blacklist_left   ENCODE_blacklist_characteristics_left   ENCODE_blacklist_right  ENCODE_blacklist_characteristics_right  ACMG    HI  TS  DDD_HI_percent  ExAC_delZ   ExAC_dupZ   ExAC_cnvZ   ExAC_synZ   ExAC_misZ   GenCC_disease   GenCC_moi   GenCC_classification    GenCC_pmid  OMIM_ID OMIM_phenotype  OMIM_inheritance    OMIM_morbid OMIM_morbid_candidate   LOEUF_bin   GnomAD_pLI  ExAC_pLI    AnnotSV_ranking_score   AnnotSV_ranking_criteria    ACMG_class

nvnieuwk commented 1 year ago

I did not set the SVinputInfo flag to 1, but it didn't work either when I did

nvnieuwk commented 1 year ago

I got it to work with another VCF file :), but still strange that it didn't work with the other one...

nvnieuwk commented 1 year ago

Hmm I'm getting the error again when testing it with another file created with the same workflow as the one that worked earlier

lgmgeo commented 1 year ago

Good news, I can reproduce your bug. It will be easier to debug. May the force be with the variantconvert developers ;o)

$ANNOTSV/bin/AnnotSV -SVinputFile test.vcf -outputFile ./test.annotated.tsv -vcf 1

nvnieuwk commented 1 year ago

Awesome! 🥳

lgmgeo commented 1 year ago

Got it!

Look at the VCF header:

#CHROM  POS ID  REF QUAL    FILTER  INFO    test1   test2   test3

It is badly formatted, no ALT and FORMAT column.

No bug in AnnotSV or variantconvert ;o)

Can you close the issue in variantconvert?

nvnieuwk commented 1 year ago

Ah! I'll change the header, but I've gotten that error with another VCF file that does have the right header so I don't think that's the issue :/

nvnieuwk commented 1 year ago

Fixing the header did seem to do the trick though, I'll investigate further what could be wrong with the other file

lgmgeo commented 1 year ago

Actually, you don't just have to modify the header. It is necessary to add the 2 ALT and FORMAT missing columns (with the missing values for each SV). AnnotSV is using the VCF format following official specification VCF v4.3.

nvnieuwk commented 1 year ago

Thank you for all the help, the columns were in that file actually. I had to add the header manually there and messed that part up somehow :).

lgmgeo / AnnotSV

VCF output returns a TSV file #168