TransVar User Guide

Contents:

• Download and Install
  • Install using pip
  • Use the docker images
  • Download the program
  • Dependency
  • Install from source
• Quick Start
• Setup and Customize
  • Use environment variables
  • Install and specify reference genome assembly
  • Install and specify transcript annotations
  • Know Current configuration
  • Set default reference builds
  • Use Additional Resources
  • Control the length of reference sequence
• Genomic level annotation
  • Short genomic regions
  • Long genomic regions
  • Genomic variant
  • Promoter region
  • Splice sites
  • UTR region
  • Non-coding RNA
  • Coding Start and Stop
  • Batch processing
• Protein level annotation
  • Protein sites
  • Protein motif
  • Protein region
  • Protein variants
  • Whole transcript
  • Search alternative codon identifiers
• cDNA level annotation
  • cDNA region
  • cDNA variant
• Interpret consequence labels (CSQN)
  • General
  • Coding Start/Stop
  • Coding Insertion/Deletion
  • Intronic
  • Intergenic
  • Splice site
  • Others
• Inspect variant sequences
  • Missense substitution
  • Deletion
  • Insertion
  • Block substitution
  • Frameshift sequence
• Using non-canonical IDs
  • Create ID Mapping File
• Output Options
  • VCF-like output
• FAQ
  • How to batch-process?
  • How to use VCF as input?
  • How to automatically decompose a haplotype into multiple mutations?
  • How to use 3-letter code instead of 1-letter code for protein?
  • How can I let TransVar output sequence context?
  • How to report results in one line for each query?
  • I got ‘gene_not_recognized’, what’s wrong?
  • Does TransVar support alternative format for MNV such as c.508_509CC>TT?
  • Does TransVar support relaxed input without ‘g.’, ‘c.’ and ‘p.’?
  • When I annotate a variant for protein identifier, why would I end up getting results in another variant type?
• Features
• Citation
• License
• Need Help

If you use TransVar in your work please cite Zhou et al. Nature Methods 12, 1002-1003 (2015). Thank you.

Indices and tables

• Index
• Module Index
• Search Page