Comments (2)
I solved the problem with a change of my reference .fasta file headers, like '>chr1 1' into '>1'.
I re-made an index file (.fai) of the changed fasta file using "samtools faidx", and ran GTCtoVCF, and it worked!
from gtctovcf.
Yes the fasta headers cannot have 'chr' if you use the download script it should remove them. Glad you fixed the issue.
from gtctovcf.
Related Issues (20)
- GTC converter - WARNING - Reference is missing entry for chromosomes HOT 8
- Precision difference when updating numpy versions
- GTC parser error : All GT values in converted vcf are './.' HOT 4
- Illumina Generated Manifest has no RefStrand column HOT 5
- Replace ID in output VCF with `--id` option
- GQ type is "String" instead of "Float" HOT 1
- download_reference.sh is outdated HOT 3
- Unable to run download_reference.sh on Mac HOT 3
- Unclear Error message HOT 1
- Next release HOT 2
- download_reference script has broken links HOT 2
- Reference not detected if lowercase characters HOT 4
- Python3 Question HOT 3
- SourceSeq validation failures should be skipped instead of erroring out
- Bus error when converting GTC to VCF HOT 7
- GQ score clarification HOT 3
- VCF REF column outputting in bytes instead of string HOT 3
- Python3 support HOT 1
- Any experience about GQ settings HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from gtctovcf.