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meth_eagle's Introduction

Meth_EAGLE

Base On EAGLE

Usage

Compile:

make

Execution:

eagle -v variants.vcf -a alignment.bam -r reference.fasta > output.tab

Detailed Description of Meth-EAGLE

Meth-EAGLE can do:

1. "variant quality scores":

  • As the general output of EAGLE, Meth-EAGLE can give "variant quality scores".

2. "methylation 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.

Meth_EAGLE Input

  • reference file
  • read file
  • varaint calling file

Meth_EAGLE Output

  • original EAGLE output
    • one file
    • variant likelihood
  • Meth-EAGLE output
    • two files
    • deamination likelihood

Floder Analysis

/data

  • 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)

/data_preprocess

  • generate_vcf.py
    • generate artificial vcf file
  • replace_sam.py
    • inserted variant information into sam file

/output

  • original EAGLE output
  • Meth-EAGLE outputs (two files)

/scripts

  • original EAGLE floder

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