Quick Start#

This 5-minute tutorial demonstrates basic WASP2 usage.

Prerequisites#

You will need:

  • A coordinate-sorted, indexed BAM file (sample.bam + sample.bam.bai)

  • A phased VCF file with heterozygous variants (variants.vcf.gz + .tbi)

These are typically produced by your alignment pipeline (BWA-MEM, STAR, etc.) followed by variant calling and phasing (GATK, WhatsHap, ShapeIt).

Count Alleles#

Count allele-specific reads from a BAM file:

wasp2-count count-variants \
  sample.bam \
  variants.vcf.gz \
  -s SAMPLE_ID \
  --out_file counts.tsv

Output: counts.tsv with columns:

  • chr, pos, ref, alt

  • ref_count, alt_count, other_count

Analyze Allelic Imbalance#

Detect significant allelic imbalance:

wasp2-analyze find-imbalance \
  counts.tsv \
  --output results.tsv

Output: results.tsv with columns:

  • region, ref_count, alt_count

  • p-value, FDR-corrected p-value

  • Statistical metrics

Interpret Results#

Significant imbalance (FDR < 0.05) indicates:

  • Preferential expression of one allele

  • Potential cis-regulatory variation

  • Technical artifacts (check coverage)

Next Steps#