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INVersions missing from the BEDPE output #98

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arnikz opened this issue Mar 21, 2022 · 0 comments
Open

INVersions missing from the BEDPE output #98

arnikz opened this issue Mar 21, 2022 · 0 comments
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@arnikz
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arnikz commented Mar 21, 2022 •
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Hi,

I ran into this issue using the vcf2bedpe.R script on the GRIDSS (v1.3.4) output:

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##ALT=<ID=INV,Description="Inversion">
##FILTER=<ID=ASSEMBLY_ONLY,Description="Variant is supported only by assembly evidence.">
##FILTER=<ID=ASSEMBLY_TOO_FEW_READ,Description="Not enough reads contribute to this assembly as specified by 'assembly.minReads'">
##FILTER=<ID=ASSEMBLY_TOO_SHORT,Description="This assembly is shorter than a read length">
##FILTER=<ID=LOW_BREAKPOINT_SUPPORT,Description="Does not reach the required threshold quality for calling as specified by 'variantcalling.minScore'">
##FILTER=<ID=LOW_QUAL,Description="Low quality call as specified by 'variantcalling.lowQuality'">
##FILTER=<ID=NO_ASSEMBLY,Description="No assembly supporting this variant could be found.">
##FILTER=<ID=REF,Description="Breakpoint corresponds to reference allele">
##FILTER=<ID=SINGLE_ASSEMBLY,Description="Only one side of the breakpoint could be assembled.">
##FILTER=<ID=SINGLE_SUPPORT,Description="Supported by a single read or read pair only.">
##FILTER=<ID=SMALL_EVENT,Description="Event size is smaller than the minimum reportable size specified by 'variantcalling.minSize'">
##FORMAT=<ID=ASQ,Number=1,Type=Float,Description="Pro-rata quality score contribution of assemblies supporting breakpoint">
##FORMAT=<ID=ASRP,Number=1,Type=Integer,Description="Count of read pairs incorporated into any breakpoint assembly">
##FORMAT=<ID=ASSR,Number=1,Type=Integer,Description="Count of split, soft clipped or indel-containing reads incorporated into any breakpoint assemblies">
##FORMAT=<ID=BAQ,Number=1,Type=Float,Description="Pro-rata quality score contribution of assemblies supporting just local breakend">
##FORMAT=<ID=BQ,Number=1,Type=Float,Description="Quality score of breakend evidence after evidence reallocation">
##FORMAT=<ID=BSC,Number=1,Type=Integer,Description="Count of soft clips supporting just local breakend per category">
##FORMAT=<ID=BSCQ,Number=1,Type=Float,Description="Quality score of soft clips supporting just local breakend per category">
##FORMAT=<ID=BUM,Number=1,Type=Integer,Description="Count of read pairs (with one read unmapped) supporting just local breakend per category">
##FORMAT=<ID=BUMQ,Number=1,Type=Float,Description="Quality score of read pairs (with one read unmapped) supporting just local breakend per category">
##FORMAT=<ID=CASQ,Number=1,Type=Float,Description="Pro-rata quality score of complex compound breakpoint assemblies supporting breakpoint from elsewhere">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=IC,Number=1,Type=Integer,Description="Count of read indels supporting breakpoint per category">
##FORMAT=<ID=IQ,Number=1,Type=Float,Description="Quality score of read indels supporting breakpoint per category">
##FORMAT=<ID=QUAL,Number=1,Type=Float,Description="Quality score of breakend evidence after evidence reallocation">
##FORMAT=<ID=RASQ,Number=1,Type=Float,Description="Pro-rata quality score contribution of assemblies supporting breakpoint from remote breakend">
##FORMAT=<ID=REF,Number=1,Type=Integer,Description="Count of reads mapping across this breakend">
##FORMAT=<ID=REFPAIR,Number=1,Type=Integer,Description="Count of reference read pairs spanning this breakpoint supporting the reference allele">
##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Count of read pairs supporting breakpoint per category">
##FORMAT=<ID=RPQ,Number=1,Type=Float,Description="Quality score of read pairs supporting breakpoint per category">
##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Count of split reads supporting breakpoint per category">
##FORMAT=<ID=SRQ,Number=1,Type=Float,Description="Quality score of split reads supporting breakpoint per category">
##INFO=<ID=AS,Number=1,Type=Integer,Description="Count of assemblies supporting breakpoint">
##INFO=<ID=ASQ,Number=1,Type=Float,Description="Quality score of assemblies supporting breakpoint">
##INFO=<ID=ASRP,Number=1,Type=Integer,Description="Count of read pairs incorporated into any breakpoint assembly">
##INFO=<ID=ASSR,Number=1,Type=Integer,Description="Count of split, soft clipped or indel-containing reads incorporated into any breakpoint assemblies">
##INFO=<ID=BA,Number=1,Type=Integer,Description="Count of assemblies supporting just local breakend">
##INFO=<ID=BAQ,Number=1,Type=Float,Description="Quality score of assemblies supporting just local breakend">
##INFO=<ID=BEID,Number=.,Type=String,Description="Breakend assemblies contributing support to the breakpoint.">
##INFO=<ID=BQ,Number=1,Type=Float,Description="Quality score of breakend evidence">
##INFO=<ID=BSC,Number=1,Type=Integer,Description="Count of soft clips supporting just local breakend">
##INFO=<ID=BSCQ,Number=1,Type=Float,Description="Quality score of soft clips supporting just local breakend">
##INFO=<ID=BUM,Number=1,Type=Integer,Description="Count of read pairs (with one read unmapped) supporting just local breakend">
##INFO=<ID=BUMQ,Number=1,Type=Float,Description="Quality score of read pairs (with one read unmapped) supporting just local breakend">
##INFO=<ID=CAS,Number=1,Type=Integer,Description="Count of complex compound breakpoint assemblies supporting breakpoint from elsewhere">
##INFO=<ID=CASQ,Number=1,Type=Float,Description="Quality score of complex compound breakpoint assemblies supporting breakpoint from elsewhere">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=CIRPOS,Number=2,Type=Integer,Description="Confidence interval around remote breakend POS for imprecise variants">
##INFO=<ID=CQ,Number=1,Type=Float,Description="Breakpoint quality score before evidence reallocation">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##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 micro-homology at event breakpoints">
##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
##INFO=<ID=IC,Number=1,Type=Integer,Description="Count of read indels supporting breakpoint">
##INFO=<ID=IHOMPOS,Number=2,Type=Integer,Description="Position of inexact homology">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=IQ,Number=1,Type=Float,Description="Quality score of read indels supporting breakpoint">
##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend">
##INFO=<ID=RAS,Number=1,Type=Integer,Description="Count of assemblies supporting breakpoint from remote breakend">
##INFO=<ID=RASQ,Number=1,Type=Float,Description="Quality score of assemblies supporting breakpoint from remote breakend">
##INFO=<ID=REF,Number=1,Type=Integer,Description="Count of reads mapping across this breakend">
##INFO=<ID=REFPAIR,Number=1,Type=Integer,Description="Count of reference read pairs spanning this breakpoint supporting the reference allele">
##INFO=<ID=RP,Number=1,Type=Integer,Description="Count of read pairs supporting breakpoint">
##INFO=<ID=RPQ,Number=1,Type=Float,Description="Quality score of read pairs supporting breakpoint">
##INFO=<ID=RSI,Number=.,Type=Integer,Description="Support interval offsets of partner breakend.">
##INFO=<ID=SC,Number=1,Type=String,Description="CIGAR for displaying anchoring alignment of any contributing evidence and microhomologies.">
##INFO=<ID=SELF,Number=0,Type=Flag,Description="Indicates a breakpoint is self-intersecting">
##INFO=<ID=SI,Number=.,Type=Integer,Description="Support interval offsets from breakend position in which at least one supporting read/read pair/assembly is mapped.">
##INFO=<ID=SR,Number=1,Type=Integer,Description="Count of split reads supporting breakpoint">
##INFO=<ID=SRQ,Number=1,Type=Float,Description="Quality score of split reads supporting breakpoint">
##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">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
##contig=<ID=10,length=135534747>
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=133851895>
##contig=<ID=13,length=115169878>
##contig=<ID=14,length=107349540>
##contig=<ID=15,length=102531392>
##contig=<ID=16,length=90354753>
##contig=<ID=17,length=81195210>
##contig=<ID=18,length=78077248>
##contig=<ID=19,length=59128983>
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##contig=<ID=MT,length=16569>
##contig=<ID=GL000207.1,length=4262>
##contig=<ID=GL000226.1,length=15008>
##contig=<ID=GL000229.1,length=19913>
##contig=<ID=GL000231.1,length=27386>
##contig=<ID=GL000210.1,length=27682>
##contig=<ID=GL000239.1,length=33824>
##contig=<ID=GL000235.1,length=34474>
##contig=<ID=GL000201.1,length=36148>
##contig=<ID=GL000247.1,length=36422>
##contig=<ID=GL000245.1,length=36651>
##contig=<ID=GL000197.1,length=37175>
##contig=<ID=GL000203.1,length=37498>
##contig=<ID=GL000246.1,length=38154>
##contig=<ID=GL000249.1,length=38502>
##contig=<ID=GL000196.1,length=38914>
##contig=<ID=GL000248.1,length=39786>
##contig=<ID=GL000244.1,length=39929>
##contig=<ID=GL000238.1,length=39939>
##contig=<ID=GL000202.1,length=40103>
##contig=<ID=GL000234.1,length=40531>
##contig=<ID=GL000232.1,length=40652>
##contig=<ID=GL000206.1,length=41001>
##contig=<ID=GL000240.1,length=41933>
##contig=<ID=GL000236.1,length=41934>
##contig=<ID=GL000241.1,length=42152>
##contig=<ID=GL000243.1,length=43341>
##contig=<ID=GL000242.1,length=43523>
##contig=<ID=GL000230.1,length=43691>
##contig=<ID=GL000237.1,length=45867>
##contig=<ID=GL000233.1,length=45941>
##contig=<ID=GL000204.1,length=81310>
##contig=<ID=GL000198.1,length=90085>
##contig=<ID=GL000208.1,length=92689>
##contig=<ID=GL000191.1,length=106433>
##contig=<ID=GL000227.1,length=128374>
##contig=<ID=GL000228.1,length=129120>
##contig=<ID=GL000214.1,length=137718>
##contig=<ID=GL000221.1,length=155397>
##contig=<ID=GL000209.1,length=159169>
##contig=<ID=GL000218.1,length=161147>
##contig=<ID=GL000220.1,length=161802>
##contig=<ID=GL000213.1,length=164239>
##contig=<ID=GL000211.1,length=166566>
##contig=<ID=GL000199.1,length=169874>
##contig=<ID=GL000217.1,length=172149>
##contig=<ID=GL000216.1,length=172294>
##contig=<ID=GL000215.1,length=172545>
##contig=<ID=GL000205.1,length=174588>
##contig=<ID=GL000219.1,length=179198>
##contig=<ID=GL000224.1,length=179693>
##contig=<ID=GL000223.1,length=180455>
##contig=<ID=GL000195.1,length=182896>
##contig=<ID=GL000212.1,length=186858>
##contig=<ID=GL000222.1,length=186861>
##contig=<ID=GL000200.1,length=187035>
##contig=<ID=GL000193.1,length=189789>
##contig=<ID=GL000194.1,length=191469>
##contig=<ID=GL000225.1,length=211173>
##contig=<ID=GL000192.1,length=547496>
##contig=<ID=NC_007605,length=171823>
##contig=<ID=hs37d5,length=35477943>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal.bam	tumor.bam
1	24927288	gridss2_9546o	G	[1:66418631[G	1056.13	PASS	AS=1;ASQ=354.94;ASRP=19;ASSR=15;BA=0;BAQ=0;BEID=asm2-26077,asm6-12617,asm6-12618;BQ=98.25;BSC=3;BSCQ=69.91;BUM=1;BUMQ=28.33;CAS=0;CASQ=0;CIPOS=0,1;CIRPOS=-1,0;CQ=1056.13;EVENT=gridss2_9546;HOMLEN=1;HOMSEQ=G;IC=0;IHOMPOS=0,1;IQ=0;PARID=gridss2_9546h;RAS=2;RASQ=396.53;REF=91;REFPAIR=42;RP=10;RPQ=196.31;SC=2X455M;SR=4;SRQ=108.35;SVTYPE=BND	GT:ASQ:ASRP:ASSR:BAQ:BQ:BSC:BSCQ:BUM:BUMQ:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ	.:0:0:0:0:0:0:0:0:0:0:0:0:0:0:42:22:0:0:0:0	.:354.94:19:15:0:98.25:3:69.91:1:28.33:0:0:0:1056.13:396.53:49:20:10:196.31:4:108.35
1	66418631	gridss2_9546h	A	[1:24927288[A	1056.13	PASS	AS=2;ASQ=396.53;ASRP=19;ASSR=15;BA=0;BAQ=0;BEID=asm2-26077,asm6-12617,asm6-12618;BQ=91.88;BSC=4;BSCQ=91.88;BUM=0;BUMQ=0;CAS=0;CASQ=0;CIPOS=-1,0;CIRPOS=0,1;CQ=1056.13;EVENT=gridss2_9546;HOMLEN=1;HOMSEQ=C;IC=0;IHOMPOS=-1,0;IQ=0;PARID=gridss2_9546o;RAS=1;RASQ=354.94;REF=1;REFPAIR=0;RP=10;RPQ=196.31;SC=2X168M110D101M;SR=4;SRQ=108.35;SVTYPE=BND	GT:ASQ:ASRP:ASSR:BAQ:BQ:BSC:BSCQ:BUM:BUMQ:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ	.:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0	.:396.53:19:15:0:91.88:4:91.88:0:0:0:0:0:1056.13:354.94:1:0:10:196.31:4:108.35

# DEBUG: added `gr` after lino. 136
$ ./vcf2bedpe.R -i gridss.vcf -l 0
GRanges object with 2 ranges and 12 metadata columns:
                seqnames            ranges strand | paramRangeID         REF
                   <Rle>         <IRanges>  <Rle> |     <factor> <character>
  gridss2_9546o        1 24927288-24927289      - |         <NA>           G
  gridss2_9546h        1 66418630-66418631      - |         <NA>           A
                          ALT      QUAL      FILTER      sourceId       partner
                  <character> <numeric> <character>   <character>   <character>
  gridss2_9546o [1:66418631[G   1056.13        PASS gridss2_9546o gridss2_9546h
  gridss2_9546h [1:24927288[A   1056.13        PASS gridss2_9546h gridss2_9546o
                     svtype     svLen      insSeq    insLen    HOMLEN
                <character> <numeric> <character> <integer> <integer>
  gridss2_9546o         INV  41491342                     0         1
  gridss2_9546h         INV  41491342                     0         1
  -------
  seqinfo: 86 sequences from an unspecified genome
[1] "SVTYPEs in BEDPE output:"

INV 
  0

$ cat gridss.bedpe
@arnikz arnikz added the bug label Mar 21, 2022
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