brentp/vcfanno issues and pull requests

#154 - vcfanno fails to parse header of bcf file

Issue - State: open - Opened by edg1983 over 1 year ago - 2 comments

#153 - Does vcfanno support NCBI RefSeq IDs?

Issue - State: closed - Opened by CynthiaChuang over 1 year ago - 2 comments

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

Issue - State: open - Opened by AaronRuben over 1 year ago - 2 comments

#151 - Unable to open...

Issue - State: closed - Opened by bgold04 almost 2 years ago - 2 comments

#150 - Release 0.3.4 missing column headers in annotated VCF

Issue - State: closed - Opened by bangbangphil almost 2 years ago - 4 comments

#149 - can annotate region info properly extend for insertion？

Issue - State: closed - Opened by liserjrqlxue over 2 years ago - 1 comment

#148 - cannot read https url

Issue - State: closed - Opened by projectoriented almost 3 years ago - 2 comments

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

Issue - State: closed - Opened by MikeHala almost 3 years ago - 5 comments

#146 - Missing annotation because of alignment problem.

Issue - State: closed - Opened by AJ2802 almost 3 years ago - 5 comments

#145 - empty output

Issue - State: closed - Opened by dKlee99 about 3 years ago - 2 comments

#143 - Failures exit with error code 0

Issue - State: closed - Opened by lbeltrame about 3 years ago - 2 comments

#142 - support for GWAS summary TSV files

Issue - State: open - Opened by darked89 about 3 years ago - 1 comment

#141 - [Typo] JavaScript function?

Issue - State: closed - Opened by thephoenixofthevoid over 3 years ago - 7 comments

#140 - Annotation header Ex. SnpEffVersion

Issue - State: open - Opened by raonyguimaraes over 3 years ago - 5 comments

#139 - Ability to add fallback / default values for fields where annotation source is missing

Issue - State: open - Opened by ssadedin over 3 years ago

#138 - Post-Annotation for new SpliceAI VCFs

Issue - State: open - Opened by Phillip-a-richmond over 3 years ago - 7 comments

#137 - CADD score not visible in the vcf annotated

Issue - State: closed - Opened by SophiaMurat over 3 years ago - 2 comments

#136 - Malformed VCF being generated -- malformed headers and whitespace

Issue - State: closed - Opened by damioresegun over 3 years ago - 6 comments

#135 - Annotating both ends of translocation

Issue - State: open - Opened by lconde-ucl over 3 years ago - 2 comments

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

Issue - State: open - Opened by vindex10 over 3 years ago - 5 comments

#133 - Filtering whilst annotating.

Issue - State: closed - Opened by tirohia almost 4 years ago - 1 comment

#132 - question about lua interface and security on a Galaxy server

Issue - State: closed - Opened by NatPRoach almost 4 years ago - 2 comments

#131 - breaking down CADD scores file into individual chromosomes

Issue - State: open - Opened by samkh918 almost 4 years ago - 4 comments

#130 - Put FILTER in FILTER field, not INFO

Issue - State: closed - Opened by bangbangphil almost 4 years ago - 3 comments

#129 - Trouble using 'first' op on dbNSFP txt file

Issue - State: open - Opened by IvantheDugtrio about 4 years ago - 5 comments

#128 - 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

Issue - State: closed - Opened by liserjrqlxue about 4 years ago - 2 comments

#127 - how to handle multi record of one allele

Issue - State: closed - Opened by liserjrqlxue about 4 years ago - 3 comments

#126 - gene set annotation from GMT file

Issue - State: open - Opened by dridk about 4 years ago

#125 - Annotations of type float slightly differ from values in the resource

Issue - State: open - Opened by bartcharbon about 4 years ago - 1 comment

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

Issue - State: open - Opened by francoiskroll about 4 years ago - 2 comments

#123 - Extra "FORMAT" in the header line

Issue - State: closed - Opened by liqg over 4 years ago - 3 comments

#122 - Errors with postannotate

Issue - State: closed - Opened by huangk3 over 4 years ago - 2 comments

#121 - working with VCF files containing SNV and CNV both like

Issue - State: open - Opened by snashraf over 4 years ago - 3 comments

#120 - VQSRTranche FILTER error

Issue - State: closed - Opened by huangk-000 over 4 years ago - 4 comments

#119 - Misleading Flatten error message

Pull Request - State: closed - Opened by tsnowlan over 4 years ago - 1 comment

#118 - Misleading error message in Flatten

Issue - State: closed - Opened by tsnowlan over 4 years ago - 2 comments

#117 - Multiple Files, Same Fields

Issue - State: closed - Opened by violetbrina over 4 years ago - 3 comments

#116 - Adding a custom value for missing annotation

Issue - State: closed - Opened by edg1983 almost 5 years ago - 9 comments

#115 - fix example table format of markdown

Pull Request - State: closed - Opened by liserjrqlxue about 5 years ago

#114 - Vcfanno does not use pipes to delimit multiple annotations for a single ALT allele

Issue - State: open - Opened by ptn24 about 5 years ago - 4 comments

#113 - Vcfanno does not typecast fields correctly when using the by_alt op

Issue - State: closed - Opened by ptn24 about 5 years ago - 6 comments

#112 - vcfanno is slient when the tabix index is older than the bed/vcf file

Issue - State: closed - Opened by zzupmc about 5 years ago - 1 comment

#111 - Annotating Breakend Points (<BND>)

Issue - State: open - Opened by ajaarma over 5 years ago - 3 comments

#110 - No X, Y, Mt chromosomes after vcfanno

Issue - State: closed - Opened by syouligan over 5 years ago - 7 comments

#109 - Fix always falling back to non-bgzip reader && allow .bgz extension

Pull Request - State: closed - Opened by zamaudio over 5 years ago - 5 comments

#108 - rs113993960 aka CFTR DeltaF508, invisible to vcfanno

Issue - State: closed - Opened by cariaso over 5 years ago - 4 comments

#107 - api.go:789: unexpected header line

Issue - State: open - Opened by BriMeireles over 5 years ago - 4 comments

#106 - Using vcfanno to annotate SV calls with GNOMAD SV frequencies

Issue - State: open - Opened by naumenko-sa over 5 years ago - 10 comments

#105 - Error with postannotation

Issue - State: closed - Opened by PedroBarbosa over 5 years ago - 5 comments

#104 - Field: FILTER not being added for gnomad annotations

Issue - State: closed - Opened by cvlvxi over 5 years ago - 10 comments

#103 - Add Makefile

Pull Request - State: closed - Opened by zamaudio over 5 years ago - 1 comment

#102 - Cannot annotate on gnomad 2.1 but working with gnomad 2.0

Issue - State: closed - Opened by cvlvxi over 5 years ago - 3 comments

#101 - Please fix the tree so it compiles

Issue - State: closed - Opened by zamaudio over 5 years ago - 1 comment

#100 - panic: interface conversion: interface {} is float64, not int

Issue - State: closed - Opened by wdecoster over 5 years ago - 5 comments

#99 - invalid memory address or nil pointer dereference

Issue - State: closed - Opened by komalsrathi over 5 years ago - 2 comments

#98 - how to add "." for variants outside intervals

Issue - State: closed - Opened by jungminchoilab over 5 years ago - 4 comments

#97 - Leading / added to filename from config file

Issue - State: closed - Opened by barrymoore almost 6 years ago - 4 comments

#96 - Add citation link

Issue - State: closed - Opened by hdashnow almost 6 years ago - 1 comment

#95 - panic: intervals out of order within file: starts at: 4294967295 and 0

Issue - State: closed - Opened by wdecoster about 6 years ago - 19 comments

#94 - Missing annotations

Issue - State: closed - Opened by Thatguy027 about 6 years ago - 17 comments

#93 - Pos(1-based) syntax error when annotation dbNSFP data

Issue - State: closed - Opened by settys02 about 6 years ago - 4 comments

#92 - Proposal for `-slightly-permission-overlap` matching pos + REF

Issue - State: closed - Opened by chapmanb about 6 years ago - 7 comments

#91 - v1.4 of CADD header with '#chr' not '#chrom'

Issue - State: closed - Opened by janakn about 6 years ago - 3 comments

#90 - Interesting failure to include annotations from .vcf.bgz instead of .vcf.gz

Issue - State: closed - Opened by Phillip-a-richmond about 6 years ago - 1 comment

#89 - Incorrect AC, AF, AN, DP values after merging multiple annotated vcfs.

Issue - State: closed - Opened by gezthxbio about 6 years ago - 1 comment

#88 - Could vcfanno annotate mutation type ? like frame-shift/Premature-Stop for indel, Synonymous/Stop_nonsyn for snp

Issue - State: closed - Opened by orangeSi over 6 years ago - 2 comments

#87 - multi allelic vcf: vcfanno is not respecting VCF number format and is flipping scores

Issue - State: open - Opened by RoanKanninga over 6 years ago - 7 comments

#86 - flag processing issue

Issue - State: closed - Opened by ferenju1 over 6 years ago - 3 comments

#85 - Produces empty INFO fields

Issue - State: closed - Opened by garrettjstevens over 6 years ago - 2 comments

#84 - CNV and SV annotation

Issue - State: closed - Opened by alphahmed18 over 6 years ago - 1 comment

#83 - multiple CADD annotations files

Issue - State: closed - Opened by RoanKanninga over 6 years ago - 8 comments

#82 - -base-path duplicates the string

Issue - State: closed - Opened by sergiigladchuk almost 7 years ago - 3 comments

#81 - allow non-standard file names

Issue - State: open - Opened by brentp almost 7 years ago - 1 comment

#80 - minor typos

Pull Request - State: closed - Opened by pdiakumis almost 7 years ago - 1 comment

#79 - max of NA returns 0

Issue - State: open - Opened by brentp almost 7 years ago

#78 - Annotate with 1000 genome data

Issue - State: closed - Opened by maggie-fu almost 7 years ago - 9 comments

#77 - Extract specific field from one column in BED

Issue - State: closed - Opened by maggie-fu almost 7 years ago - 1 comment

#76 - Feature request - specify annotation file paths at runtime

Issue - State: closed - Opened by jdidion almost 7 years ago - 1 comment

#75 - Change field type for BED file annotation

Issue - State: closed - Opened by maggie-fu almost 7 years ago - 1 comment

#74 - custom lua error- reciprocal overlap

Issue - State: closed - Opened by maggie-fu about 7 years ago - 5 comments

#73 - feature request - indicate annotation file has a subset of chroms

Issue - State: open - Opened by drmjc about 7 years ago - 1 comment

#72 - Go vendoring?

Issue - State: open - Opened by ilovezfs about 7 years ago - 3 comments

#71 - api.go:263: WARNING: out of bounds with ref: [T], alt: [A T], vals: [%!s(int=227542)]

Issue - State: closed - Opened by alig99 over 7 years ago - 8 comments

#70 - GEMINI configuration: match latest ClinVar

Pull Request - State: closed - Opened by chapmanb over 7 years ago

#69 - Change header ##INFO description to "Number=A"?

Issue - State: closed - Opened by garrettjstevens over 7 years ago - 5 comments

#68 - Separator of multiple hits and allele specific flag

Issue - State: closed - Opened by kyasuno over 7 years ago - 25 comments

#67 - Feature: read from stdin

Issue - State: closed - Opened by matthdsm over 7 years ago - 2 comments

#66 - Compressed VCF/BCF output

Issue - State: closed - Opened by dancooke over 7 years ago - 1 comment

#65 - Recognising reserved INFO fields

Issue - State: open - Opened by dancooke over 7 years ago - 2 comments

#64 - vcfanno gzip IO related errors (race condition with multiple threads to bgzf.Reader)

Issue - State: closed - Opened by chapmanb over 7 years ago - 9 comments

#63 - Custom postannotation description

Issue - State: open - Opened by liqg over 7 years ago - 1 comment

#62 - better gene annotation

Issue - State: open - Opened by brentp over 7 years ago

#57 - api.go:655: tabix: name count mismatch:

Issue - State: closed - Opened by sergiigladchuk over 7 years ago - 2 comments

GitHub / brentp/vcfanno issues and pull requests