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We would like to add [LINSIGHT](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5395419/) into the annotation pipeline for the hg38 version of crg2 to predict the fitness consequences of non-coding mutat…
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Hi there,
I merged four SV callers using svdb merge (delly, smoove, manta, tiddit). Then I tried running the merged VCF through vcfanno to annotate with genomic features and ran into an error. I ch…
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### Description of feature
Currently the workflow uses the VEP cache for annotation, but should also enable using local files from databases for annotation. Hence, other database sources can be added…
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We should build the system for allowing access to local vcf files. We will also need a way to specify where these files are for local users. But, here are operations that we need:
1. Given a database,…
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Hi
We're very pleased with vcfanno performance but we found some modifications in the final vcf that annoys us a little.
Basically, vcfanno rounds out "QUAL" to 1 decimal point (from 2 in the origin…
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I tried your tool to convert vep annotated vcf to table, it worked great except one column was messed up:
`VEP_MOTIF_SCORE_CHANGE`.
I annotated the vcf with vep and then vcfanno, the entries added…
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Where are conservation scores coming from?
It would be great to have all clinvar annotations; gene.iobio does that separately now
Let's look at what gnomAD vcf files we are using in annotateVariants…
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Hello,
I tried to run vcfanno with my files (grch37.vcfanno.conf and out-ensemble.vcf.gz) and also tried to run your example (tests/testVA/). Both times, I found the same error:
- Command that I …
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Hi
I am trying to use a GTF file to annotate the VCF. I do not find a use case so I just tried with my best guess:
```
[[annotation]]
file="/home/mpschr/bin/bcbionextgen/data/genomes/Hsapiens/…
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More like a suggestion. I think it would be awesome to have this included. We could run e.g. vcfanno, which is very fast and provide the users with an annotation (in terms of gene space) together with…