Quick Start#

This 5-minute tutorial demonstrates basic WASP2 usage.

Example Data#

Use the included test data:

cd WASP2-exp
ls test_data/

Count Alleles#

Count allele-specific reads from a BAM file:

wasp2-count count-variants \
  test_data/CD4_ATACseq_Day1_merged_filtered.sort.bam \
  test_data/filter_chr10.vcf \
  --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#