Supplementary Figure 5: The WASP combined haplotype test pipeline.
From: WASP: allele-specific software for robust molecular quantitative trait locus discovery
Mapped reads (in BAM or SAM format) for each individual, genotypes for known SNPs, and a list of regions and SNPs to test are provided to WASP. WASP extracts read counts for the target regions as well as allele-specific read counts. Read counts from multiple sources can be used to update heterozygous probabilities. Expected read counts for each region are adjusted through modeling of the relationships between read counts and GC content and between read counts and total read counts for each sample. Dispersion parameters are estimated from the data and provided to the combined haplotype test along with the read counts. Principal components can optionally be used as covariates by the test.
