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I am trying to use PyVCF to write a simple script that filters VCF records based on certain criteria. However, this script seems to break the header of my VCF file, as bcftools no longer parses the re…
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Each annotation has a specific usage protocol that needs to be included when you do the page configuration. ie. g or f
When you submit the config page a separate array should be added that contains t…
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Hello,
I found that if I use default parameter for hgvs annotation some lines have more fields than others.
This is because when the variant is on multiple NM, multiple hgvs are separated by a tabula…
viv-1 updated
9 years ago
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Connect config options to code so that annovar is executed from the configured path. Also, when querying use the max results from config options.
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As discussed in our meeting, variant documents should be indexed by the fields that will be used to filter them.
Proposed variant collection indexes:
- chromosome, position
- all AF annotations
- eff…
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Comments are invited on the initial draft of the variant annotation API
https://github.com/ga4gh/schemas/tree/variation_annotation
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# Issues to address with vcf uploads that we have come across
### Processing non standard vcf files
1. Should the the pipeline try to coerce the incoming vcf file into a standard format
2. How do you …
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Hello,
I tried to upload a VCF file (3.7 MB) which has caused _Failed: Bad Request (400)_ with the following Dockerfile:
```
FROM bgruening/galaxy-stable:dev
MAINTAINER auto script
ENV GALAXY_CONFIG_…
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This idea needs careful thought of affected architecture
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See in which intron a variant is found. Should you have to go to IGV?