WASP2: Allele-Specific Analysis#
WASP2 is a comprehensive suite of tools for unbiased allele-specific analysis of next-generation sequencing data. It addresses reference bias in read mapping and provides statistical methods for detecting allelic imbalance.
Features#
Unbiased Mapping: WASP algorithm for correcting reference bias
Allele Counting: Count allele-specific reads from BAM files
Statistical Analysis: Beta-binomial models for allelic imbalance detection
Single-Cell Support: Specialized tools for single-cell RNA-seq
Type-Safe: 100% type hint coverage for robust code
Well-Tested: Comprehensive regression and integration tests
Quick Start#
Install via pip:
pip install wasp2
Count alleles from a BAM file:
wasp2-count count-variants sample.bam variants.vcf
Analyze allelic imbalance:
wasp2-analyze find-imbalance counts.tsv
Documentation#
Getting Started
Tutorials
- Quickstart: Count Alleles in 5 Minutes
- Quickstart: WASP Mapping Filter
- RNA-seq Allelic Imbalance Tutorial
- 10X scRNA-seq Tutorial
- Single-Cell ATAC-seq Workflow
- Comparative Imbalance Analysis Tutorial
- ATAC-seq Allelic Imbalance Analysis Tutorial
- Statistical Methods Tutorial: Understanding WASP2’s Beta-Binomial Framework
- Prerequisites
- Relationship to WASP2 Source Code
- Critical Constants and Helper Functions
- Section 1: Understanding Overdispersion
- Section 2: The Beta-Binomial Distribution
- Section 3: Dispersion Estimation
- Section 4: QQ Plots for Model Calibration
- Section 5: False Discovery Rate (FDR) Correction
- Summary
Statistical Methods
API Reference