brentp vcfanno issues - Githubissues

brentp / vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0973-5

MIT License

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issues

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QUAL & GNOMAD rounded out

#159 jomoxi opened 1 month ago
2
Release a binary for Linux ARM64

#158 martin-g closed 9 months ago
2
Filtering variants by CADD value or nonsynonymous_SNV from annotated VCF file with Annovar

#157 alanmejiamaza closed 11 months ago
2
Tolerant VCF parsing

#156 drtconway opened 12 months ago
3
Resolving ambiguity in multiallelic sites

#155 e-271 opened 1 year ago
0
vcfanno fails to parse header of bcf file

#154 edg1983 opened 1 year ago
2
Does vcfanno support NCBI RefSeq IDs?

#153 CynthiaChuang closed 1 year ago
2
vcfanno doesn't annotate sites that are polymorphic in query vcf but fixed for reference allele in annotation vcf

#152 AaronRuben opened 1 year ago
2
Unable to open...

#151 bgold04 closed 1 year ago
2
Release 0.3.4 missing column headers in annotated VCF

#150 bangbangphil closed 1 year ago
4
can annotate region info properly extend for insertion？

#149 liserjrqlxue closed 2 years ago
1
cannot read https url

#148 projectoriented closed 2 years ago
2
CADD score not visible in the vcf annotated (similar to #137 )

#147 MikeHala closed 2 years ago
5
Missing annotation because of alignment problem.

#146 AJ2802 closed 2 years ago
5
empty output

#145 dKlee99 closed 2 years ago
2
Failures exit with error code 0

#143 lbeltrame closed 3 years ago
2
support for GWAS summary TSV files

#142 darked89 opened 3 years ago
1
[Typo] JavaScript function?

#141 thephoenixofthevoid closed 3 years ago
7
Annotation header Ex. SnpEffVersion

#140 raonyguimaraes opened 3 years ago
5
Ability to add fallback / default values for fields where annotation source is missing

#139 ssadedin opened 3 years ago
0
Post-Annotation for new SpliceAI VCFs

#138 Phillip-a-richmond opened 3 years ago
8
CADD score not visible in the vcf annotated

#137 SophiaMurat closed 3 years ago
2
Malformed VCF being generated -- malformed headers and whitespace

#136 damioresegun closed 3 years ago
6
Annotating both ends of translocation

#135 lconde-ucl opened 3 years ago
2
error: index out of range. when FORMAT field is provided but no sample columns present

#134 vindex10 opened 3 years ago
5
Filtering whilst annotating.

#133 tirohia closed 3 years ago
1
question about lua interface and security on a Galaxy server

#132 NatPRoach closed 3 years ago
2
breaking down CADD scores file into individual chromosomes

#131 samkh918 opened 3 years ago
4
Put FILTER in FILTER field, not INFO

#130 bangbangphil closed 3 years ago
3
Trouble using 'first' op on dbNSFP txt file

#129 IvantheDugtrio opened 3 years ago
5
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 liserjrqlxue closed 3 years ago
2
how to handle multi record of one allele

#127 liserjrqlxue closed 3 years ago
3
gene set annotation from GMT file

#126 dridk opened 4 years ago
0
Annotations of type float slightly differ from values in the resource

#125 bartcharbon opened 4 years ago
1
How to extract fields that are not ##INFO from gnomAD vcf?

#124 francoiskroll opened 4 years ago
2
Extra "FORMAT" in the header line

#123 liqg closed 1 year ago
3
Errors with postannotate

#122 huangk3 closed 4 years ago
2
working with VCF files containing SNV and CNV both like

#121 snashraf opened 4 years ago
3
VQSRTranche FILTER error

#120 huangk-000 closed 4 years ago
4
Misleading Flatten error message

#119 tsnowlan closed 4 years ago
1
Misleading error message in Flatten

#118 tsnowlan closed 4 years ago
2
Multiple Files, Same Fields

#117 violetbrina closed 4 years ago
3
Adding a custom value for missing annotation

#116 edg1983 closed 4 years ago
9
fix example table format of markdown

#115 liserjrqlxue closed 4 years ago
0
Vcfanno does not use pipes to delimit multiple annotations for a single ALT allele

#114 ptn24 opened 5 years ago
4
Vcfanno does not typecast fields correctly when using the by_alt op

#113 ptn24 closed 5 years ago
6
vcfanno is slient when the tabix index is older than the bed/vcf file

#112 zzupmc closed 5 years ago
1
Annotating Breakend Points (<BND>)

#111 ajaarma opened 5 years ago
3
No X, Y, Mt chromosomes after vcfanno

#110 syouligan closed 5 years ago
7
Fix always falling back to non-bgzip reader && allow .bgz extension

#109 zamaudio closed 5 years ago
5