TAPES : a Tool for Assessment and Prioritisation in Exome Studies

Please refer to the WIKI for more information on all TAPES functions.
See HERE for installation and dependencies resolutions.

The command perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar avdblist ./ does not seem to download the list of databases available for ANNOVAR anymore (this might be temporary). If this happens, please download:
https://github.com/a-xavier/tapes/files/5507866/hg19_avdblist.txt
and
https://github.com/a-xavier/tapes/files/5507867/hg38_avdblist.txt
and place them in your ANNOVAR folder (where annotate_variation.pl is located).

TAPES is an open-source tool written in python3 designed to predict pathogenicity of variants in exome studies. It is especially designed for small scalle exome studies (from dozens to a few hundreds) sharing a common trait/phenotype. TAPES can also handle trio data with healthy parents and calculate variant enrichment compared to the general population wwithout the use of controls.

Have an awesome idea, correction, feedback for TAPES? Want to contribute, please add an entry in the Issues or a Pull Request.

Unnanotated VCF --Annotate--> Annotated VCF --Sort--> Reports
TAPES recommanded input is a multi-sample vcf or bcf file.

Follow the instructions here to try TAPES' workflow using a toy dataset.

TAPES can be used as an ANNOVAR wrapper for easy VCF/gzipped VCF/BCF annotation (this requires to download ANNOVAR).

python3 tapes.py db -s -A /path/to/annovar/ to scan the annovar path for existing databases
python3 tapes.py db -b --acmg -a hg19 to download all necessary databases
python3 tapes.py annotate -i /path/to/variant_file.bcf -o /path/to/annotated_file.vcf --amcg to annotate the bcf or vcf file of interest

TAPES can predict the pathogenicity of variants (using ANNOVAR or VEP annotated VCF):

• by assigning the ACMG/AMP Criteria
• provide a probability (from 0 to 1) of a variant to be pathogenic based on Tavtigian et al model

python3 tapes.py sort -i /path/to/annotated_file.vcf -o /path/to/output/ --tab
to sort and prioritise an annotated vcf.

TAPES can calculate the enrichment of variants in a population sharing the same phenotype without the need for controls, using public databases and extrapolating the number of individuals affected/non-affected by a variant using Minor Allele Frequencies from public databases.
Check the details HERE.

TAPES provides an array of useful reports on top of the main report (which will prioritise variants based on predicted pathogenicity)

• --list python3 tapes.py sort -i /path/to/annotated_file.vcf -o /path/to/output/ --by_gene
  to filter the main report with a user-supplied gene symbol list.
• --disease python3 tapes.py sort -i /path/to/annotated_file.vcf -o /path/to/output/ --by_gene
  to filter the main report based on a disease characteristics (eg. 'autosomal dominant' or 'colorectal')
• --kegg python3 tapes.py sort -i /path/to/annotated_file.vcf -o /path/to/output/ --by_gene to filter the main report based on a kegg pathway (eg. "Pathways in cancer" or "base excision repair")

python3 tapes.py sort -i /path/to/annotated_file.vcf -o /path/to/output/ --by_gene
to create a by gene report with an associated gene mutational burden score.

python3 tapes.py sort -i /path/to/annotated_file.vcf -o /path/to/output/ --enrichr GO_Biological_Process_2018
to perfome pathway analysis with genes containing pathogenic variants.

python3 tapes.py sort -i /path/to/annotated_file.vcf -o /path/to/output/ --by_sample
to create a table of the most pathogenic variants per individual.

• Support for VEP annotated vcf and BS2 criteria assignment optimisation Done
• Add --by_gene report to files with only one sample. Done
• Better enrichement calculation for PS4 criteria assignment Done
• Output VCF files
• Analysing InterVar output files
• Using real control samples for OR calculation/PS4
• Docker image creation
• Polygenic Risk Score calculation without controls

If you use TAPES, please cite the reference paper:

Xavier A, Scott RJ, Talseth-Palmer BA (2019) TAPES: A tool for assessment and prioritisation in exome studies. PLOS Computational Biology 15(10): e1007453. https://doi.org/10.1371/journal.pcbi.1007453