brentp/vcfanno

Issues

• Filtering variants by CADD value or nonsynonymous_SNV from annotated VCF file with Annovar

  #157 opened 9 months ago by alanmejiamaza
  2

• Tolerant VCF parsing

  #156 opened 9 months ago by drtconway
  3

• Resolving ambiguity in multiallelic sites

  #155 opened 10 months ago by e-271
  0

• vcfanno fails to parse header of bcf file

  #154 opened a year ago by edg1983
  2

• Does vcfanno support NCBI RefSeq IDs?

  #153 opened a year ago by CynthiaChuang
  2

• vcfanno doesn't annotate sites that are polymorphic in query vcf but fixed for reference allele in annotation vcf

  #152 opened a year ago by AaronRuben
  2

• Unable to open...

  #151 opened a year ago by bgold04
  2

• Release 0.3.4 missing column headers in annotated VCF

  #150 opened 2 years ago by bangbangphil
  4

• Extra "FORMAT" in the header line

  #123 opened 2 years ago by liqg
  3

• error: index out of range. when FORMAT field is provided but no sample columns present

  #134 opened 3 years ago by vindex10
  5

• Post-Annotation for new SpliceAI VCFs

  #138 opened 3 years ago by Phillip-a-richmond
  7

• can annotate region info properly extend for insertion？

  #149 opened 2 years ago by liserjrqlxue
  1

• cannot read https url

  #148 opened 2 years ago by projectoriented
  2

• CADD score not visible in the vcf annotated (similar to #137 )

  #147 opened 2 years ago by MikeHala
  5

• Annotation header Ex. SnpEffVersion

  #140 opened 3 years ago by raonyguimaraes
  5

• Missing annotation because of alignment problem.

  #146 opened 3 years ago by AJ2802
  5

• empty output

  #145 opened 3 years ago by dKlee99
  2

• Failures exit with error code 0

  #143 opened 3 years ago by lbeltrame
  2

• support for GWAS summary TSV files

  #142 opened 3 years ago by darked89
  1

• [Typo] JavaScript function?

  #141 opened 3 years ago by thephoenixofthevoid
  7

• Ability to add fallback / default values for fields where annotation source is missing

  #139 opened 3 years ago by ssadedin
  0

• CADD score not visible in the vcf annotated

  #137 opened 3 years ago by SophiaMurat
  2

• Malformed VCF being generated -- malformed headers and whitespace

  #136 opened 3 years ago by damioresegun
  6

• Annotating both ends of translocation

  #135 opened 3 years ago by lconde-ucl
  2

• Filtering whilst annotating.

  #133 opened 3 years ago by tirohia
  1

• question about lua interface and security on a Galaxy server

  #132 opened 3 years ago by NatPRoach
  2

• breaking down CADD scores file into individual chromosomes

  #131 opened 4 years ago by samkh918
  4

• Trouble using 'first' op on dbNSFP txt file

  #129 opened 4 years ago by IvantheDugtrio
  5

• Put FILTER in FILTER field, not INFO

  #130 opened 4 years ago by bangbangphil
  3

• does this warning mater?| WARNING: using op 'self' when with Number='1' can result in out-of-order values when the query is multi-allelic

  #128 opened 4 years ago by liserjrqlxue
  2

• how to handle multi record of one allele

  #127 opened 4 years ago by liserjrqlxue
  3

• gene set annotation from GMT file

  #126 opened 4 years ago by dridk
  0

• Annotations of type float slightly differ from values in the resource

  #125 opened 4 years ago by bartcharbon
  1

• How to extract fields that are not ##INFO from gnomAD vcf?

  #124 opened 4 years ago by francoiskroll
  2

• Errors with postannotate

  #122 opened 4 years ago by huangk3
  2

• Multiple Files, Same Fields

  #117 opened 4 years ago by violetbrina
  3

• working with VCF files containing SNV and CNV both like

  #121 opened 4 years ago by snashraf
  3

• Adding a custom value for missing annotation

  #116 opened 4 years ago by edg1983
  9

• VQSRTranche FILTER error

  #120 opened 4 years ago by huangk-000
  4

• Misleading error message in Flatten

  #118 opened 4 years ago by tsnowlan
  2

• Using vcfanno to annotate SV calls with GNOMAD SV frequencies

  #106 opened 5 years ago by naumenko-sa
  10

• Field: FILTER not being added for gnomad annotations

  #104 opened 5 years ago by cvlvxi
  10

• Vcfanno does not typecast fields correctly when using the by_alt op

  #113 opened 5 years ago by ptn24
  6

• Vcfanno does not use pipes to delimit multiple annotations for a single ALT allele

  #114 opened 5 years ago by ptn24
  4

• vcfanno is slient when the tabix index is older than the bed/vcf file

  #112 opened 5 years ago by zzupmc
  1

• Annotating Breakend Points (<BND>)

  #111 opened 5 years ago by ajaarma
  3

• No X, Y, Mt chromosomes after vcfanno

  #110 opened 5 years ago by syouligan
  7

• api.go:789: unexpected header line

  #107 opened 5 years ago by BriMeireles
  4

• rs113993960 aka CFTR DeltaF508, invisible to vcfanno

  #108 opened 5 years ago by cariaso
  4

• Error with postannotation

  #105 opened 5 years ago by PedroBarbosa
  5