So, first off, as others have pointed out, I'm pretty sure that example is just wrong. At least, the numbers don't match as you've pointed out.
That said, it is impossible to be sure without showing us the header of the VCF file as well. The INFO field (the 5th field of a VCF file) is very, very variable and depends entirely on the header lines. Each program (or human) implementing a VCF is free to choose to have whatever they feel like in the INFO field. However, each IDENTIFIER=
needs to have an associated INFO line at the beginning of the file.
So, the SVTYPE
, SVLEN
, HOMLEN
etc will have commented (start with a #
) lines at the beginning of the file explaining what these values are. So check those, even though they're relatively standard, you never know, the obvious reading you used might be wrong despite its seeming so reasonable.
Here's a newer example of a VCF line for an SV taken from the current VCF specification:
##fileformat=VCFv4.1
##fileDate=20100501
##reference=1000GenomesPilot-NCBI36
##assembly=ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/sv/breakpoint_assemblies.fasta
##INFO=<ID=BKPTID,Number=.,Type=String,Description="ID of the assembled alternate allele in the assembly file">
##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=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##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=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">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
##ALT=<ID=DEL:ME:L1,Description="Deletion of L1 element">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=DUP:TANDEM,Description="Tandem Duplication">
##ALT=<ID=INS,Description="Insertion of novel sequence">
##ALT=<ID=INS:ME:ALU,Description="Insertion of ALU element">
##ALT=<ID=INS:ME:L1,Description="Insertion of L1 element">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=CNV,Description="Copy number variable region">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype quality">
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001
1 2827694 rs2376870 CGTGGATGCGGGGAC C . PASS SVTYPE=DEL;END=2827708;HOMLEN=1;HOMSEQ=G;SVLEN=-14 GT:GQ 1/1:13.9
Note how the numbers do match and also note how each of the subfields in the INFO field is explained with an ##INFO
line.
END
value is simply wrong in that example. Maybe send the info@ email address a note regarding this so they can fix it. $\endgroup$