Allele-specific Methylation

Allele-specific methylation can be extracted from the pairwise epiread files via:

biscuit epiread -@ NTHREADS -P -B snps.bed \
    /path/to/my_reference.fa my_output.bam | \
sort -k1,1 -k2,2n -k3,3n my_output.pairwise > my_output.sorted.pairwise

biscuit asm my_output.sorted.pairwise > my_output.asm

An example of the .asm file format is:

chr11    2132802    2132844    T/C    T/C    0    1    2    0    3.333333e-01    8.326452e-02
chr11    2132851    2132804    T/C    T/C    1    0    0    1    1.000000e+00    1.572992e-01

The columns represent:

1. Chromosome name
2. SNP location
3. CpG location
4. SNP₁/SNP₂ (SNPs for row₁/row₂ in contingency table)
5. CpG₁/CpG₂ (CpGs for col₁/col₂ in contingency table)
6. SNP₁-CpG₁ count (contingency table value in row₁-col₁)
7. SNP₁-CpG₂ count (contingency table value in row₁-col₂)
8. SNP₂-CpG₁ count (contingency table value in row₂-col₁)
9. SNP₂-CpG₂ count (contingency table value in row₂-col₂)
10. Two-tail Fisher’s exact p-value
11. χ² p-value