variant analysis

Prediction of the functional effects of genetic variants

variant_calling

Identifies genetic variants such as SNPs, indels, and structural variations from sequencing data.

Usage:

import GenBioX.variant_analysis as va

va.ariant_calling(input_bam, reference_genome, output_vcf)

Annotates genetic variants with information such as gene annotation, variant type, location, and allele frequency.

Usage:

va.variant_annotation(input_vcf, output_annovar_prefix, database)

Predicts the functional consequences of genetic variants

Usage:

va.variant_effect_prediction(input_vcf, output_vcf, reference_genome)

predicts the effect of variants on splicing by analyzing splice site sequences and motifs

Usage:

va.splice_site_prediction(input_vcf, output_vcf, reference_genome):

predicts the effect of variants on phenotypes

Usage:

va.phenotype_prediction(variants, phenotypes)