Annotation of Identified Variants to Create Reports for Clinicians to Assist Therapeutic Decisions
It requires three main modules: pandas, myvariant and reportlab
pip install pandas
pip install myvariant
pip install reportlab
pip install aiv
pip install aiv --upgrade
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')
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
- Performance can be determined by calculating the running time for a given input file with 6000+ mutations.