- https://github.com/tony-kuo/eagle
- Kuo, T., Frith, M. C., Sese, J., & Horton, P. (2018). EAGLE: Explicit Alternative Genome Likelihood Evaluator. BMC Medical Genomics, 11, [28]. https://doi.org/10.1186/s12920-018-0342-1
make
eagle -v variants.vcf -a alignment.bam -r reference.fasta > output.tab
- As the general output of EAGLE, Meth-EAGLE can give "variant quality scores".
- To remove the bias which may be generated by variants, Meth-EAGLE modifies the given reference sequence by the best variant set calculated by the previous procedure.
- Supposing all CpG sites are the potential methylated cites, Meth-EAGLE uses this modified reference sequence to calculate the "methylation quality scores" of all CpG sites.
- reference file
- read file
- varaint calling file
- original EAGLE output
- one file
- variant likelihood
- Meth-EAGLE output
- two files
- deamination likelihood
- ref file (artificial data)
- vcf file (generated by myself, in 'data_preprocess' floder)
- bam file (already sorted)
- sam file (inserted variant information by myself, in 'data_preprocess' floder)
- .ch3 file (generated by simulator)
- read file (generated by simulator)
- generate_vcf.py
- generate artificial vcf file
- replace_sam.py
- inserted variant information into sam file
- original EAGLE output
- Meth-EAGLE outputs (two files)
- original EAGLE floder