aiv 0.4.3

A variant annotation package

AIV: Annotation of Identified Variants

Annotation of Identified Variants to Create Reports for Clinicians to Assist Therapeutic Decisions

Prerequisites

It requires three main modules: pandas, myvariant and reportlab

pip install pandas
pip install myvariant
pip install reportlab

Installation

pip install aiv

Upgrade

pip install aiv --upgrade

Usage

import aiv

# Get variant info 
aiv.getvariant('chr1', 69635, 'G', 'C')

# Annotate variants, reference genome: hg38
aiv.annotate_mutations('variant_calls.tsv', assembly='hg38')

# Annotate variants, reference genome: hg19
aiv.annotate_mutations('bwa_mutect2_nb09_50_lines.txt', assembly='hg19')

Tests

You can test your installation with sample variant call files. Input test files can be found at:

./tests/test_annotate_variants.tsv
./tests/bwa_mutect2_nb09_50_lines.txt
./tests/my_data.txt

Input File Format

Report Preview

Future Work

• Performance can be determined by calculating the running time for a given input file with 6000+ mutations.