Version Compatibility

Reference examples tested with: WASP 0.3.4+, GATK 4.4+, RASQUAL 1.1+, samtools 1.19+, bcftools 1.19+, vcftools 0.1.16+, plink 2.00+, MatrixEQTL 2.3+, QuASAR 0.1+, bowtie2 2.5+, bwa-mem2 2.2.1+, scipy 1.11+ (false_discovery_control), pandas 2+, pybedtools 0.10+.

Verify before use:

• CLI: <tool> --version then <tool> --help to confirm flags
• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws unexpected errors, introspect the installed package and adapt rather than retrying.

Allele-Specific Accessibility

"Does this heterozygous SNP affect chromatin accessibility on its allele?" -> Count ATAC reads supporting reference vs alternative allele at heterozygous sites in the same individual; significant deviation from 50:50 indicates cis-regulatory effect. Requires careful handling of reference-allele mapping bias (WASP filtering) and within-individual binomial testing.

• CLI: WASP (Geijn 2015) for de-biased reference mapping
• CLI: gatk ASEReadCounter for allele-specific count tables
• CLI: RASQUAL (Kumasaka 2016) for joint cis-mapping with allelic counts
• R: QuASAR (Harvey 2015) for genotype + ASE inference simultaneously