/usr/lib/python2.7/dist-packages/pbsuite/utils/vcfTemplates/SVTemplate.vcf is in python-pbsuite-utils 15.8.24+dfsg-2.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | ##fileformat=VCFv4.1
##fileDate=20100501
##reference=1000GenomesPilot-NCBI36
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=NoSpan,Description="No reads properly spanned for consensus building">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
##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">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=INS,Description="Insertion of sequence">
##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=COV,Number=1,Type=Integer,Description="Region Average Coverage">
##FORMAT=<ID=ALT,Number=2,Type=Integer,Description="Number of variant reads per-strand (+,-)">
##FORMAT=<ID=ALNID,Number=1,Type=Float,Description="Estimated consensus sequence identity">
##FORMAT=<ID=MQF,Number=1,Type=Integer,Description="Number of reads filtered for low mapping 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">
##FORMAT=<ID=ZMW,Number=1,Type=Integer,Description="Number of ZMWs Supporing Variant">
##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Average length of remaining sequence between breakpoints">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
1 2827694 rs2376870 CGTGGATGCGGGGAC C . PASS SVTYPE=DEL;END=2827762;HOMLEN=1;HOMSEQ=G;SVLEN=-68 GT:GQ 1/1:13.9
2 321682 . T <DEL> 6 PASS SVTYPE=DEL;END=321887;SVLEN=-205;CIPOS=-56,20;CIEND=-10,62 GT:GQ 0/1:12
2 14477084 . C <DEL> 12 PASS SVTYPE=DEL;END=14477381;SVLEN=-297;CIPOS=-22,18;CIEND=-12,32 GT:GQ 0/1:12
3 9425916 . C <INS> 23 PASS SVTYPE=INS;END=9425916;SVLEN=6027;CIPOS=-16,22 GT:GQ 1/1:15
3 12665100 . A <CNV> 14 PASS SVTYPE=DUP;END=12686200;SVLEN=21100;CIPOS=-500,500;CIEND=-500,500 GT:GQ:CN:CNQ ./.:0:3:16.2
4 18665128 . T <CNV> 11 PASS SVTYPE=DUP;END=18665204;SVLEN=76;CIPOS=-10,10;CIEND=-10,10 GT:GQ:CN:CNQ ./.:0:5:8.3
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