|
1 | 1 | ##fileformat=VCFv4.2 |
2 | | -##FILTER=<ID=PASS,Description="All filters passed"> |
3 | | -##5UTR_annotation=Variant annotation from UTRAnnotator |
4 | | -##5UTR_consequence=Variant consequence from UTRAnnotator |
5 | | -##CADD_PHRED=PHRED-like scaled CADD score. CADD is only available here for non-commercial use. See CADD website for more information. |
6 | | -##CADD_RAW=Raw CADD score. CADD is only available here for non-commercial use. See CADD website for more information. |
7 | | -##Existing_InFrame_oORFs=The number of existing inFrame overlapping ORFs (inFrame oORF) at the 5 prime UTR |
8 | | -##Existing_OutOfFrame_oORFs=The number of existing out-of-frame overlapping ORFs (OutOfFrame oORF) at the 5 prime UTR |
9 | | -##Existing_uORFs=The number of existing uORFs with a stop codon within the 5 prime UTR |
10 | | -##FILTER=<ID=EXCESS_ALLELES,Description="Site has an excess of alternate alleles based on the input threshold"> |
11 | | -##FILTER=<ID=ExcessHet,Description="Site has excess het value larger than the threshold"> |
12 | 2 | ##FILTER=<ID=LowQual,Description="Low quality"> |
13 | 3 | ##FILTER=<ID=NO_HQ_GENOTYPES,Description="Site has no high quality variant genotypes"> |
14 | | -##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> |
15 | | -##FORMAT=<ID=FT,Number=.,Type=String,Description="Genotype-level filter"> |
16 | | -##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> |
17 | | -##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> |
18 | | -##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles"> |
19 | | -##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> |
20 | | -##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)"> |
21 | | -##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)"> |
22 | 4 | ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> |
23 | 5 | ##INFO=<ID=AC_Hemi,Number=A,Type=Integer,Description="Allele counts in hemizygous genotypes"> |
24 | 6 | ##INFO=<ID=AC_Het,Number=A,Type=Integer,Description="Allele counts in heterozygous genotypes"> |
25 | 7 | ##INFO=<ID=AC_Hom,Number=A,Type=Integer,Description="Allele counts in homozygous genotypes"> |
26 | 8 | ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> |
27 | 9 | ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> |
28 | 10 | ##INFO=<ID=AS_QUALapprox,Number=1,Type=String,Description="Allele-specific QUAL approximations"> |
29 | | -##INFO=<ID=CALIBRATION_SENSITIVITY,Number=A,Type=String,Description="Calibration sensitivity corresponding to the value of SCORE"> |
30 | | -##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|GENE_PHENO|NEAREST|HGVS_OFFSET|AF|CLIN_SIG|SOMATIC|PHENO|REVEL|SpliceRegion|CADD_PHRED|CADD_RAW|5UTR_annotation|5UTR_consequence|Existing_InFrame_oORFs|Existing_OutOfFrame_oORFs|Existing_uORFs|SpliceAI_pred_DP_AG|SpliceAI_pred_DP_AL|SpliceAI_pred_DP_DG|SpliceAI_pred_DP_DL|SpliceAI_pred_DS_AG|SpliceAI_pred_DS_AL|SpliceAI_pred_DS_DG|SpliceAI_pred_DS_DL|SpliceAI_pred_SYMBOL"> |
31 | | -##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> |
32 | | -##INFO=<ID=F_MISSING,Number=.,Type=Float,Description="Added by +fill-tags expression F_MISSING=F_MISSING"> |
33 | | -##INFO=<ID=OLD_MULTIALLELIC,Number=1,Type=String,Description="Original chr:pos:ref:alt encoding"> |
34 | | -##INFO=<ID=OLD_VARIANT,Number=.,Type=String,Description="Original chr:pos:ref:alt encoding"> |
35 | | -##INFO=<ID=QUALapprox,Number=1,Type=Integer,Description="Sum of PL[0] values; used to approximate the QUAL score"> |
36 | | -##INFO=<ID=SCORE,Number=A,Type=String,Description="Score according to the model applied by ScoreVariantAnnotations"> |
37 | | -##INFO=<ID=TYPE,Number=.,Type=String,Description="Variant type"> |
38 | | -##REVEL=Rare Exome Variant Ensemble Learner |
39 | | -##SpliceAI_pred_DP_AG=SpliceAI predicted effect on splicing. Delta position for acceptor gain |
40 | | -##SpliceAI_pred_DP_AL=SpliceAI predicted effect on splicing. Delta position for acceptor loss |
41 | | -##SpliceAI_pred_DP_DG=SpliceAI predicted effect on splicing. Delta position for donor gain |
42 | | -##SpliceAI_pred_DP_DL=SpliceAI predicted effect on splicing. Delta position for donor loss |
43 | | -##SpliceAI_pred_DS_AG=SpliceAI predicted effect on splicing. Delta score for acceptor gain |
44 | | -##SpliceAI_pred_DS_AL=SpliceAI predicted effect on splicing. Delta score for acceptor loss |
45 | | -##SpliceAI_pred_DS_DG=SpliceAI predicted effect on splicing. Delta score for donor gain |
46 | | -##SpliceAI_pred_DS_DL=SpliceAI predicted effect on splicing. Delta score for donor loss |
47 | | -##SpliceAI_pred_SYMBOL=SpliceAI gene symbol |
48 | | -##SpliceRegion=SpliceRegion predictions |
49 | 11 | ##contig=<ID=chr14,length=107043718> |
50 | | -##high_CALIBRATION_SENSITIVITY_INDEL=Sample Genotype FT filter value indicating that the genotyped allele failed INDEL model calibration sensitivity cutoff (0.99) |
51 | | -##high_CALIBRATION_SENSITIVITY_SNP=Sample Genotype FT filter value indicating that the genotyped allele failed SNP model calibration sensitivity cutoff (0.997) |
52 | 12 | ##source=SelectVariants |
53 | 13 | ##INFO=<ID=VRS_Allele_IDs,Number=R,Type=String,Description="The computed identifiers for the GA4GH VRS Alleles corresponding to the GT indexes of the REF and ALT alleles"> |
54 | | -##INFO=<ID=VRS_Error,Number=.,Type=String,Description="If an error occurred computing a VRS Identifier, the error message"> |
55 | | -##INFO=<ID=VRS_Starts,Number=R,Type=String,Description="Interresidue coordinates used as the location starts for the GA4GH VRS Alleles corresponding to the GT indexes of the REF and ALT alleles"> |
56 | | -##INFO=<ID=VRS_Ends,Number=R,Type=String,Description="Interresidue coordinates used as the location ends for the GA4GH VRS Alleles corresponding to the GT indexes of the REF and ALT alleles"> |
57 | | -##INFO=<ID=VRS_States,Number=R,Type=String,Description="The literal sequence states used for the GA4GH VRS Alleles corresponding to the GT indexes of the REF and ALT alleles"> |
58 | 14 | #CHROM POS ID REF ALT QUAL FILTER INFO |
59 | | -chr14 18223529 . C A . LowQual;NO_HQ_GENOTYPES AC=0;AC_Hemi=0;AC_Het=0;AC_Hom=0;AF=0.00;AN=0;AS_QUALapprox=0|55;CALIBRATION_SENSITIVITY=.;CSQ=A|intergenic_variant|MODIFIER|||||||||||||||rs1294420531||||||||OR11H12||||||||3.503|0.321010||||||||||||||;F_MISSING=0.23692;QUALapprox=55;SCORE=.;TYPE=SNP;VRS_Allele_IDs=ga4gh:VA.8OSPHYmhyg9hJTpFQ8aNcmLgYMR77ZyJ,ga4gh:VA.slgr2fnRKaUnQrJZvYNDGMrfZHw6QCr6;VRS_Starts=18223528,18223528;VRS_Ends=18223529,18223529;VRS_States=C,A |
| 15 | +chr14 18223529 . C A . LowQual;NO_HQ_GENOTYPES AC=0;AC_Hemi=0;AC_Het=0;AC_Hom=0;AF=0.00;AN=0;AS_QUALapprox=0|55;VRS_Allele_IDs=ga4gh:VA.8OSPHYmhyg9hJTpFQ8aNcmLgYMR77ZyJ,ga4gh:VA.slgr2fnRKaUnQrJZvYNDGMrfZHw6QCr6 |
0 commit comments