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Last active August 29, 2015 14:03
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Jannovar Error
Raw
shell.sh
git clone git@github.com:charite/jannovar.git
cd jannovar
mvn install
# SUCCESS
java -jar target/jannovar-0.6-SNAPSHOT.jar --create-refseq
java -jar target/jannovar-0.6-SNAPSHOT.jar -D data/refseq_hg19.ser -U data -g hg19 -V subset_vcfBeta-HG00731-200-37-ASM.vcf
#Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: 2
# at java.lang.String.charAt(String.java:658)
# at jannovar.annotation.BlockSubstitution.getAnnotationBlockPlusStrand(BlockSubstitution.java:158)
# at jannovar.reference.Chromosome.annotateExonicVariants(Chromosome.java:777)
# at jannovar.reference.Chromosome.getPlusStrandAnnotation(Chromosome.java:434)
# at jannovar.reference.Chromosome.getAnnotationList(Chromosome.java:169)
# at jannovar.Jannovar.annotateVCFLine(Jannovar.java:378)
# at jannovar.Jannovar.outputAnnotatedVCF(Jannovar.java:485)
# at jannovar.Jannovar.annotateVCF(Jannovar.java:600)
# at jannovar.Jannovar.main(Jannovar.java:250)
java -jar target/jannovar-0.6-SNAPSHOT.jar -D data/refseq_hg19.ser -U data -g hg19 -V trio_ceu_vcfBeta-NA19240-200-37-ASM.vcf
#Exception in thread "main" java.lang.NullPointerException
# at jannovar.annotation.BlockSubstitution.getAnnotationBlockPlusStrand(BlockSubstitution.java:149)
# at jannovar.reference.Chromosome.annotateExonicVariants(Chromosome.java:778)
# at jannovar.reference.Chromosome.getMinusStrandAnnotation(Chromosome.java:647)
# at jannovar.reference.Chromosome.getAnnotationList(Chromosome.java:172)
# at jannovar.Jannovar.annotateVCFLine(Jannovar.java:394)
# at jannovar.Jannovar.outputAnnotatedVCF(Jannovar.java:508)
# at jannovar.Jannovar.annotateVCF(Jannovar.java:623)
# at jannovar.Jannovar.main(Jannovar.java:254)
Raw
subset_vcfBeta-HG00731-200-37-ASM.vcf
##fileformat=VCFv4.1
##fileDate=20120730
##center=Complete Genomics
##source=CGAPipeline_2.0.0.26;cgatools_1.6.0
##source_GENOME_REFERENCE=NCBI build 37
##source_GENE_ANNOTATIONS=NCBI build 37.2
##source_DBSNP_BUILD=dbSNP build 132
##source_COSMIC=COSMIC v48
##source_DGV_VERSION=9
##source_MIRBASE_VERSION=miRBase version 16
##source_PFAM_DATE=April 21, 2011
##source_REPMASK_GENERATED_AT=2011-Feb-15 10:08
##source_SEGDUP_GENERATED_AT=2010-Dec-01 13:40
##phasing=partial
##source_MAX_PLOIDY=10
##source_NUMBER_LEVELS=GS00392-DNA_A01:7
##source_NONDIPLOID_WINDOW_WIDTH=100000
##source_MEAN_GC_CORRECTED_CVG=GS00392-DNA_A01:48.73
##source_MEI_1000G_ANNOTATIONS=INITIAL-DATA-RELEASE
##reference=ftp://ftp.completegenomics.com/ReferenceFiles/build37.fa.bz2
##contig=<ID=1,length=249250621,assembly=B37,md5=1b22b98cdeb4a9304cb5d48026a85128,species="Homo sapiens">
##contig=<ID=2,length=243199373,assembly=B37,md5=a0d9851da00400dec1098a9255ac712e,species="Homo sapiens">
##contig=<ID=3,length=198022430,assembly=B37,md5=641e4338fa8d52a5b781bd2a2c08d3c3,species="Homo sapiens">
##contig=<ID=4,length=191154276,assembly=B37,md5=23dccd106897542ad87d2765d28a19a1,species="Homo sapiens">
##contig=<ID=5,length=180915260,assembly=B37,md5=0740173db9ffd264d728f32784845cd7,species="Homo sapiens">
##contig=<ID=6,length=171115067,assembly=B37,md5=1d3a93a248d92a729ee764823acbbc6b,species="Homo sapiens">
##contig=<ID=7,length=159138663,assembly=B37,md5=618366e953d6aaad97dbe4777c29375e,species="Homo sapiens">
##contig=<ID=8,length=146364022,assembly=B37,md5=96f514a9929e410c6651697bded59aec,species="Homo sapiens">
##contig=<ID=9,length=141213431,assembly=B37,md5=3e273117f15e0a400f01055d9f393768,species="Homo sapiens">
##contig=<ID=10,length=135534747,assembly=B37,md5=988c28e000e84c26d552359af1ea2e1d,species="Homo sapiens">
##contig=<ID=11,length=135006516,assembly=B37,md5=98c59049a2df285c76ffb1c6db8f8b96,species="Homo sapiens">
##contig=<ID=12,length=133851895,assembly=B37,md5=51851ac0e1a115847ad36449b0015864,species="Homo sapiens">
##contig=<ID=13,length=115169878,assembly=B37,md5=283f8d7892baa81b510a015719ca7b0b,species="Homo sapiens">
##contig=<ID=14,length=107349540,assembly=B37,md5=98f3cae32b2a2e9524bc19813927542e,species="Homo sapiens">
##contig=<ID=15,length=102531392,assembly=B37,md5=e5645a794a8238215b2cd77acb95a078,species="Homo sapiens">
##contig=<ID=16,length=90354753,assembly=B37,md5=fc9b1a7b42b97a864f56b348b06095e6,species="Homo sapiens">
##contig=<ID=17,length=81195210,assembly=B37,md5=351f64d4f4f9ddd45b35336ad97aa6de,species="Homo sapiens">
##contig=<ID=18,length=78077248,assembly=B37,md5=b15d4b2d29dde9d3e4f93d1d0f2cbc9c,species="Homo sapiens">
##contig=<ID=19,length=59128983,assembly=B37,md5=1aacd71f30db8e561810913e0b72636d,species="Homo sapiens">
##contig=<ID=20,length=63025520,assembly=B37,md5=0dec9660ec1efaaf33281c0d5ea2560f,species="Homo sapiens">
##contig=<ID=21,length=48129895,assembly=B37,md5=2979a6085bfe28e3ad6f552f361ed74d,species="Homo sapiens">
##contig=<ID=22,length=51304566,assembly=B37,md5=a718acaa6135fdca8357d5bfe94211dd,species="Homo sapiens">
##contig=<ID=X,length=155270560,assembly=B37,md5=7e0e2e580297b7764e31dbc80c2540dd,species="Homo sapiens">
##contig=<ID=Y,length=59373566,assembly=B37,md5=1e86411d73e6f00a10590f976be01623,species="Homo sapiens">
##contig=<ID=M,length=16569,assembly=B37,md5=c68f52674c9fb33aef52dcf399755519,species="Homo sapiens">
##ALT=<ID=CGA_NOCALL,Description="No-called record">
##ALT=<ID=CGA_CNVWIN,Description="Copy number analysis window">
##ALT=<ID=INS:ME:ALU,Description="Insertion of ALU element">
##ALT=<ID=INS:ME:L1,Description="Insertion of L1 element">
##ALT=<ID=INS:ME:SVA,Description="Insertion of SVA element">
##ALT=<ID=INS:ME:MER,Description="Insertion of MER element">
##ALT=<ID=INS:ME:LTR,Description="Insertion of LTR element">
##ALT=<ID=INS:ME:PolyA,Description="Insertion of PolyA element">
##ALT=<ID=INS:ME:HERV,Description="Insertion of HERV element">
##FILTER=<ID=VQLOW,Description="Quality not VQHIGH">
##FILTER=<ID=SQLOW,Description="Somatic quality not SQHIGH">
##FILTER=<ID=URR,Description="Too close to an underrepresented repeat">
##FILTER=<ID=MPCBT,Description="Mate pair count below 10">
##FILTER=<ID=SHORT,Description="Junction side length below 70">
##FILTER=<ID=TSNR,Description="Transition sequence not resolved">
##FILTER=<ID=INTERBL,Description="Interchromosomal junction in baseline">
##FILTER=<ID=sns75,Description="Sensitivity to known MEI calls in range (.75,.95] i.e. medium FDR">
##FILTER=<ID=sns95,Description="Sensitivity to known MEI calls in range (.95,1.00] i.e. high to very high FDR">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele">
##INFO=<ID=CGA_XR,Number=A,Type=String,Description="Per-ALT external database reference (dbSNP, COSMIC, etc)">
##INFO=<ID=CGA_FI,Number=A,Type=String,Description="Functional impact annotation">
##INFO=<ID=CGA_PFAM,Number=.,Type=String,Description="PFAM Domain">
##INFO=<ID=CGA_MIRB,Number=.,Type=String,Description="miRBaseId">
##INFO=<ID=CGA_RPT,Number=.,Type=String,Description="repeatMasker overlap information">
##INFO=<ID=CGA_SDO,Number=1,Type=Integer,Description="Number of distinct segmental duplications that overlap this locus">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=CGA_WINEND,Number=1,Type=Integer,Description="End of coverage window">
##INFO=<ID=CGA_BF,Number=1,Type=Float,Description="Frequency in baseline">
##INFO=<ID=CGA_MEDEL,Number=4,Type=String,Description="Consistent with deletion of mobile element; type,chromosome,start,end">
##INFO=<ID=MATEID,Number=1,Type=String,Description="ID of mate breakend">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=CGA_BNDG,Number=A,Type=String,Description="Transcript name and strand of genes containing breakend">
##INFO=<ID=CGA_BNDGO,Number=A,Type=String,Description="Transcript name and strand of genes containing mate breakend">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=MEINFO,Number=4,Type=String,Description="Mobile element info of the form NAME,START,END,POLARITY">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phase Set">
##FORMAT=<ID=SS,Number=1,Type=String,Description="Somatic Status: Germline, Somatic, LOH, or . (Unknown)">
##FORMAT=<ID=FT,Number=1,Type=String,Description="Genotype filters">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
##FORMAT=<ID=EHQ,Number=2,Type=Integer,Description="Haplotype Quality, Equal Allele Fraction Assumption">
##FORMAT=<ID=CGA_CEHQ,Number=2,Type=Integer,Description="Calibrated Haplotype Quality, Equal Allele Fraction Assumption">
##FORMAT=<ID=GL,Number=.,Type=Integer,Description="Genotype Likelihood">
##FORMAT=<ID=CGA_CEGL,Number=.,Type=Integer,Description="Calibrated Genotype Likelihood, Equal Allele Fraction Asssumption">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Read Depth">
##FORMAT=<ID=AD,Number=2,Type=Integer,Description="Allelic depths (number of reads in each observed allele)">
##FORMAT=<ID=CGA_RDP,Number=1,Type=Integer,Description="Number of reads observed supporting the reference allele">
##FORMAT=<ID=CGA_GP,Number=1,Type=Float,Description="Depth of coverage for 2k window GC normalized to mean">
##FORMAT=<ID=CGA_NP,Number=1,Type=Float,Description="Coverage for 2k window, GC-corrected and normalized relative to copy-number-corrected multi-sample baseline">
##FORMAT=<ID=CGA_CL,Number=1,Type=Float,Description="Nondiploid-model called level">
##FORMAT=<ID=CGA_LS,Number=1,Type=Integer,Description="Nondiploid-model called level score">
##FORMAT=<ID=CGA_CP,Number=1,Type=Integer,Description="Diploid-model called ploidy">
##FORMAT=<ID=CGA_PS,Number=1,Type=Integer,Description="Diploid-model called ploidy score">
##FORMAT=<ID=CGA_CT,Number=1,Type=String,Description="Diploid-model CNV type">
##FORMAT=<ID=CGA_TS,Number=1,Type=Integer,Description="Diploid-model CNV type score">
##FORMAT=<ID=CGA_BNDMPC,Number=1,Type=Integer,Description="Mate pair count supporting breakend">
##FORMAT=<ID=CGA_BNDPOS,Number=1,Type=Integer,Description="Breakend position">
##FORMAT=<ID=CGA_BNDDEF,Number=1,Type=String,Description="Breakend definition">
##FORMAT=<ID=CGA_BNDP,Number=1,Type=String,Description="Precision of breakend">
##FORMAT=<ID=CGA_IS,Number=1,Type=Float,Description="MEI InsertionScore: confidence in occurrence of an insertion">
##FORMAT=<ID=CGA_IDC,Number=1,Type=Float,Description="MEI InsertionDnbCount: count of paired ends supporting insertion">
##FORMAT=<ID=CGA_IDCL,Number=1,Type=Float,Description="MEI InsertionLeftDnbCount: count of paired ends supporting insertion on 5' end of insertion point">
##FORMAT=<ID=CGA_IDCR,Number=1,Type=Float,Description="MEI InsertionRightDnbCount: count of paired ends supporting insertion on 3' end of insertion point">
##FORMAT=<ID=CGA_RDC,Number=1,Type=Integer,Description="MEI ReferenceDnbCount: count of paired ends supporting reference allele">
##FORMAT=<ID=CGA_NBET,Number=1,Type=String,Description="MEI NextBestElementType: (sub)type of second-most-likely inserted mobile element">
##FORMAT=<ID=CGA_ETS,Number=1,Type=Float,Description="MEI ElementTypeScore: confidence that insertion is of type indicated by CGA_ET/ElementType">
##FORMAT=<ID=CGA_KES,Number=1,Type=Float,Description="MEI KnownEventSensitivityForInsertionScore: fraction of known MEI insertion polymorphisms called for this sample with CGA_IS at least as high as for the current call">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00731-200-37-ASM
5 139060383 . GCG GTGGTA . . NS=1;AN=2;AC=1;CGA_FI=51523|NM_016463.7|CXXC5|CDS|INSERT+ GT:PS:FT:GQ:HQ:EHQ:CGA_CEHQ:GL:CGA_CEGL:DP:AD:CGA_RDP 1/0:.:PASS:79:79,79:68,68:14,21:-79,0,-79:-14,0,-21:18:4,14:14
Raw
trio_ceu_vcfBeta-NA19240-200-37-ASM.vcf
##fileformat=VCFv4.1
##fileDate=20120730
##center=Complete Genomics
##source=CGAPipeline_2.0.0.26;cgatools_1.6.0
##source_GENOME_REFERENCE=NCBI build 37
##source_GENE_ANNOTATIONS=NCBI build 37.2
##source_DBSNP_BUILD=dbSNP build 132
##source_COSMIC=COSMIC v48
##source_DGV_VERSION=9
##source_MIRBASE_VERSION=miRBase version 16
##source_PFAM_DATE=April 21, 2011
##source_REPMASK_GENERATED_AT=2011-Feb-15 10:08
##source_SEGDUP_GENERATED_AT=2010-Dec-01 13:40
##phasing=partial
##source_MAX_PLOIDY=10
##source_NUMBER_LEVELS=GS00706-DNA_C01:5
##source_NONDIPLOID_WINDOW_WIDTH=100000
##source_MEAN_GC_CORRECTED_CVG=GS00706-DNA_C01:70.43
##source_MEI_1000G_ANNOTATIONS=INITIAL-DATA-RELEASE
##reference=ftp://ftp.completegenomics.com/ReferenceFiles/build37.fa.bz2
##contig=<ID=1,length=249250621,assembly=B37,md5=1b22b98cdeb4a9304cb5d48026a85128,species="Homo sapiens">
##contig=<ID=2,length=243199373,assembly=B37,md5=a0d9851da00400dec1098a9255ac712e,species="Homo sapiens">
##contig=<ID=3,length=198022430,assembly=B37,md5=641e4338fa8d52a5b781bd2a2c08d3c3,species="Homo sapiens">
##contig=<ID=4,length=191154276,assembly=B37,md5=23dccd106897542ad87d2765d28a19a1,species="Homo sapiens">
##contig=<ID=5,length=180915260,assembly=B37,md5=0740173db9ffd264d728f32784845cd7,species="Homo sapiens">
##contig=<ID=6,length=171115067,assembly=B37,md5=1d3a93a248d92a729ee764823acbbc6b,species="Homo sapiens">
##contig=<ID=7,length=159138663,assembly=B37,md5=618366e953d6aaad97dbe4777c29375e,species="Homo sapiens">
##contig=<ID=8,length=146364022,assembly=B37,md5=96f514a9929e410c6651697bded59aec,species="Homo sapiens">
##contig=<ID=9,length=141213431,assembly=B37,md5=3e273117f15e0a400f01055d9f393768,species="Homo sapiens">
##contig=<ID=10,length=135534747,assembly=B37,md5=988c28e000e84c26d552359af1ea2e1d,species="Homo sapiens">
##contig=<ID=11,length=135006516,assembly=B37,md5=98c59049a2df285c76ffb1c6db8f8b96,species="Homo sapiens">
##contig=<ID=12,length=133851895,assembly=B37,md5=51851ac0e1a115847ad36449b0015864,species="Homo sapiens">
##contig=<ID=13,length=115169878,assembly=B37,md5=283f8d7892baa81b510a015719ca7b0b,species="Homo sapiens">
##contig=<ID=14,length=107349540,assembly=B37,md5=98f3cae32b2a2e9524bc19813927542e,species="Homo sapiens">
##contig=<ID=15,length=102531392,assembly=B37,md5=e5645a794a8238215b2cd77acb95a078,species="Homo sapiens">
##contig=<ID=16,length=90354753,assembly=B37,md5=fc9b1a7b42b97a864f56b348b06095e6,species="Homo sapiens">
##contig=<ID=17,length=81195210,assembly=B37,md5=351f64d4f4f9ddd45b35336ad97aa6de,species="Homo sapiens">
##contig=<ID=18,length=78077248,assembly=B37,md5=b15d4b2d29dde9d3e4f93d1d0f2cbc9c,species="Homo sapiens">
##contig=<ID=19,length=59128983,assembly=B37,md5=1aacd71f30db8e561810913e0b72636d,species="Homo sapiens">
##contig=<ID=20,length=63025520,assembly=B37,md5=0dec9660ec1efaaf33281c0d5ea2560f,species="Homo sapiens">
##contig=<ID=21,length=48129895,assembly=B37,md5=2979a6085bfe28e3ad6f552f361ed74d,species="Homo sapiens">
##contig=<ID=22,length=51304566,assembly=B37,md5=a718acaa6135fdca8357d5bfe94211dd,species="Homo sapiens">
##contig=<ID=X,length=155270560,assembly=B37,md5=7e0e2e580297b7764e31dbc80c2540dd,species="Homo sapiens">
##contig=<ID=Y,length=59373566,assembly=B37,md5=1e86411d73e6f00a10590f976be01623,species="Homo sapiens">
##contig=<ID=M,length=16569,assembly=B37,md5=c68f52674c9fb33aef52dcf399755519,species="Homo sapiens">
##ALT=<ID=CGA_NOCALL,Description="No-called record">
##ALT=<ID=CGA_CNVWIN,Description="Copy number analysis window">
##ALT=<ID=INS:ME:ALU,Description="Insertion of ALU element">
##ALT=<ID=INS:ME:L1,Description="Insertion of L1 element">
##ALT=<ID=INS:ME:SVA,Description="Insertion of SVA element">
##ALT=<ID=INS:ME:MER,Description="Insertion of MER element">
##ALT=<ID=INS:ME:LTR,Description="Insertion of LTR element">
##ALT=<ID=INS:ME:PolyA,Description="Insertion of PolyA element">
##ALT=<ID=INS:ME:HERV,Description="Insertion of HERV element">
##FILTER=<ID=VQLOW,Description="Quality not VQHIGH">
##FILTER=<ID=SQLOW,Description="Somatic quality not SQHIGH">
##FILTER=<ID=URR,Description="Too close to an underrepresented repeat">
##FILTER=<ID=MPCBT,Description="Mate pair count below 10">
##FILTER=<ID=SHORT,Description="Junction side length below 70">
##FILTER=<ID=TSNR,Description="Transition sequence not resolved">
##FILTER=<ID=INTERBL,Description="Interchromosomal junction in baseline">
##FILTER=<ID=sns75,Description="Sensitivity to known MEI calls in range (.75,.95] i.e. medium FDR">
##FILTER=<ID=sns95,Description="Sensitivity to known MEI calls in range (.95,1.00] i.e. high to very high FDR">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele">
##INFO=<ID=CGA_XR,Number=A,Type=String,Description="Per-ALT external database reference (dbSNP, COSMIC, etc)">
##INFO=<ID=CGA_FI,Number=A,Type=String,Description="Functional impact annotation">
##INFO=<ID=CGA_PFAM,Number=.,Type=String,Description="PFAM Domain">
##INFO=<ID=CGA_MIRB,Number=.,Type=String,Description="miRBaseId">
##INFO=<ID=CGA_RPT,Number=.,Type=String,Description="repeatMasker overlap information">
##INFO=<ID=CGA_SDO,Number=1,Type=Integer,Description="Number of distinct segmental duplications that overlap this locus">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=CGA_WINEND,Number=1,Type=Integer,Description="End of coverage window">
##INFO=<ID=CGA_BF,Number=1,Type=Float,Description="Frequency in baseline">
##INFO=<ID=CGA_MEDEL,Number=4,Type=String,Description="Consistent with deletion of mobile element; type,chromosome,start,end">
##INFO=<ID=MATEID,Number=1,Type=String,Description="ID of mate breakend">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=CGA_BNDG,Number=A,Type=String,Description="Transcript name and strand of genes containing breakend">
##INFO=<ID=CGA_BNDGO,Number=A,Type=String,Description="Transcript name and strand of genes containing mate breakend">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=MEINFO,Number=4,Type=String,Description="Mobile element info of the form NAME,START,END,POLARITY">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phase Set">
##FORMAT=<ID=SS,Number=1,Type=String,Description="Somatic Status: Germline, Somatic, LOH, or . (Unknown)">
##FORMAT=<ID=FT,Number=1,Type=String,Description="Genotype filters">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
##FORMAT=<ID=EHQ,Number=2,Type=Integer,Description="Haplotype Quality, Equal Allele Fraction Assumption">
##FORMAT=<ID=CGA_CEHQ,Number=2,Type=Integer,Description="Calibrated Haplotype Quality, Equal Allele Fraction Assumption">
##FORMAT=<ID=GL,Number=.,Type=Integer,Description="Genotype Likelihood">
##FORMAT=<ID=CGA_CEGL,Number=.,Type=Integer,Description="Calibrated Genotype Likelihood, Equal Allele Fraction Asssumption">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Read Depth">
##FORMAT=<ID=AD,Number=2,Type=Integer,Description="Allelic depths (number of reads in each observed allele)">
##FORMAT=<ID=CGA_RDP,Number=1,Type=Integer,Description="Number of reads observed supporting the reference allele">
##FORMAT=<ID=CGA_GP,Number=1,Type=Float,Description="Depth of coverage for 2k window GC normalized to mean">
##FORMAT=<ID=CGA_NP,Number=1,Type=Float,Description="Coverage for 2k window, GC-corrected and normalized relative to copy-number-corrected multi-sample baseline">
##FORMAT=<ID=CGA_CL,Number=1,Type=Float,Description="Nondiploid-model called level">
##FORMAT=<ID=CGA_LS,Number=1,Type=Integer,Description="Nondiploid-model called level score">
##FORMAT=<ID=CGA_CP,Number=1,Type=Integer,Description="Diploid-model called ploidy">
##FORMAT=<ID=CGA_PS,Number=1,Type=Integer,Description="Diploid-model called ploidy score">
##FORMAT=<ID=CGA_CT,Number=1,Type=String,Description="Diploid-model CNV type">
##FORMAT=<ID=CGA_TS,Number=1,Type=Integer,Description="Diploid-model CNV type score">
##FORMAT=<ID=CGA_BNDMPC,Number=1,Type=Integer,Description="Mate pair count supporting breakend">
##FORMAT=<ID=CGA_BNDPOS,Number=1,Type=Integer,Description="Breakend position">
##FORMAT=<ID=CGA_BNDDEF,Number=1,Type=String,Description="Breakend definition">
##FORMAT=<ID=CGA_BNDP,Number=1,Type=String,Description="Precision of breakend">
##FORMAT=<ID=CGA_IS,Number=1,Type=Float,Description="MEI InsertionScore: confidence in occurrence of an insertion">
##FORMAT=<ID=CGA_IDC,Number=1,Type=Float,Description="MEI InsertionDnbCount: count of paired ends supporting insertion">
##FORMAT=<ID=CGA_IDCL,Number=1,Type=Float,Description="MEI InsertionLeftDnbCount: count of paired ends supporting insertion on 5' end of insertion point">
##FORMAT=<ID=CGA_IDCR,Number=1,Type=Float,Description="MEI InsertionRightDnbCount: count of paired ends supporting insertion on 3' end of insertion point">
##FORMAT=<ID=CGA_RDC,Number=1,Type=Integer,Description="MEI ReferenceDnbCount: count of paired ends supporting reference allele">
##FORMAT=<ID=CGA_NBET,Number=1,Type=String,Description="MEI NextBestElementType: (sub)type of second-most-likely inserted mobile element">
##FORMAT=<ID=CGA_ETS,Number=1,Type=Float,Description="MEI ElementTypeScore: confidence that insertion is of type indicated by CGA_ET/ElementType">
##FORMAT=<ID=CGA_KES,Number=1,Type=Float,Description="MEI KnownEventSensitivityForInsertionScore: fraction of known MEI insertion polymorphisms called for this sample with CGA_IS at least as high as for the current call">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA19240-L2-200-37-ASM
4 780267 . G . . . NS=1;AN=1 GT:PS:FT:HQ:EHQ:CGA_CEHQ:GL:CGA_CEGL 0|.:780267:PASS:51,.:38,.:0,.:0:0
4 780270 . G . . . NS=1;AN=0 GT:PS ./.:.
4 780280 . CGCGCGCGGC CGCGCGGGGC . . NS=1;AN=1;AC=1;CGA_XR=dbsnp.120|rs10794536;CGA_FI=100129917|NR_036511.1|LOC100129917|TSS-UPSTREAM|UNKNOWN-INC&100129917|NR_036512.1|LOC100129917|TSS-UPSTREAM|UNKNOWN-INC&10815|NM_006651.3|CPLX1|CDS|NO-CHANGE&10815|NM_006651.3|CPLX1|UTR3|UNKNOWN-INC GT:PS:FT:HQ:EHQ:CGA_CEHQ:GL:CGA_CEGL:DP:AD:CGA_RDP 1|.:780267:PASS:58,.:45,.:19,.:-58,0,0:-19,0,0:8:1,.:0
4 780308 . T . . . NS=1;AN=0 GT:PS ./.:.
4 780358 . CTCCTCCTCCACCTCGTCCCCGCAG . . . NS=1;AN=0 GT:PS ./.:.
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