MutAnno

MutAnno is a python toolkit providing variant annotations based on a command line interface.

pip install mutanno
mutanno annot -vcf test.vcf -out test.annot.vcf

Contents

• 1. Installation
  • 1.1. Prerequisites
  • 1.2. Install with pypi
  • 1.3. Install with code from github
• 2. Optional arguments
  • 2.1. Run annotation (annot)
  • 2.2. Make a single data source file (makedata)
  • 2.3. Convert file format (convert)
• 3. Download Data Source (download)
  • 3.1. Datasource List
  • 3.2. Download methods
  • 3.3. Variant annotation
    • 3.3.1. VEP
  • 3.4. Population data
    • 3.4.1. dbSNP
    • 3.4.2. gnomAD
    • 3.4.3. UK10K
  • 3.5. Conservation
    • 3.5.1. GERP
    • 3.5.2. PHASTCONS
    • 3.5.3. PHYLOP
    • 3.5.4. SIPHY
  • 3.6. Pathogenicity
    • 3.6.1. CADD
    • 3.6.2. SpliceAI
  • 3.7. Variant database
    • 3.7.1. CLINVAR
    • 3.7.2. COSMIC
  • 3.8. Gene annotation
    • 3.8.1. ENSEMBLgene
    • 3.8.2. ENSEMBLgeneGRCh37
    • 3.8.3. CYTOBAND
    • 3.8.4. RefSeq
    • 3.8.5. HGNC
    • 3.8.6. ClinGen
    • 3.8.7. ClinGenDisease
    • 3.8.8. ENSEMBLIDxrefTrscriptID
    • 3.8.9. ENSEMBLIDxref
    • 3.8.10. dbNSFP
    • 3.8.11. gnomADmetrics
    • 3.8.12. Marrvel
    • 3.8.13. CassaNatGenet2017
    • 3.8.14. GTEx
    • 3.8.15. BrainSpan
    • 3.8.16. BrainAtlas
    • 3.8.17. GenCode
• 4. Data Source Version
  • 4.1. GRCh38 (hg38)
    • 4.1.1. Variant annotation
    • 4.1.2. Gene annotation
  • 4.2. GRCh37 (hg19)
    • 4.2.1. Variant annotation
    • 4.2.2. Gene annotation
• 5. Make Single Source File (makedata)
  • 5.1. Input file
    • 5.1.1. Data structure file
    • 5.1.2. Data source file
  • 5.2. Output file
  • 5.3. Annotation type
    • 5.3.1. SNV
    • 5.3.2. GENE
    • 5.3.3. CODING_GENE_MAIN_CHROM
  • 5.4. Only for specific genomic region
• 6. Annotate Variants (annot)
  • 6.1. Input file
    • 6.1.1. VCF file (-vcf)
    • 6.1.2. Data source file (-sourcefile)
    • 6.1.3. Data structure file (-ds)
  • 6.2. Output file
    • 6.2.1. Annotated output file (-out)
    • 6.2.2. Out file type (-outtype)
  • 6.3. Split multi-allelic variant into single allelic variant (-split_multi_allelic_variant)
  • 6.4. Add additional information
    • 6.4.1. Add genotype (-genoinfo)
    • 6.4.2. Add hg19 coordinates (-hg19)
  • 6.5. Remove annotation tag
• 7. Annotate Gene (annot)
• 8. Data Structure File
  • 8.1. Basic strcture
  • 8.2. Root attributes
  • 8.3. Source attributes
  • 8.4. Field attributes
• 9. Data Structure File Version
  • 9.1. Variant Data Structure
  • 9.2. Gene Data Structure
• 10. Annotated VCF file format
  • 10.1. VCF-Specific Restrictions
  • 10.2. Requirements
  • 10.3. Separator Summary
  • 10.4. Example
  • 10.5. Item Generation
• 11. Run Command in CGAP Project
  • 11.1. Make Single Data Source File
    • 11.1.1. Run VEP
    • 11.1.2. Download and Preprocess Source for Micro Annotation
    • 11.1.3. Download and Preprocess Source for Full Annotation
    • 11.1.4. Download Data Source for Gene Annotation
  • 11.2. Convert VEP to .mti for novel InDels
    • 11.2.1. Run VEP
    • 11.2.2. Make Additional .mti for Novel InDels
    • 11.2.3. Make Additional .mti for Novel InDels
  • 11.3. Annotation
    • 11.3.1. Run Micro-Annotation
    • 11.3.2. Run Full-Annotation
  • 11.4. Gene annotation
• 12. Benchmark
• 13. Version History
  • 13.1. v0.4.x release series
  • 13.2. v0.3.x release series