Guillermo Barturen, Antonio Rueda, José L. Oliver and Michael Hackenberg
For questions and feedback, please contact to: MH - firstname.lastname@example.org, JLO - email@example.com, GB - firstname.lastname@example.org
News and releases
Fixed a bug related to perl versions below 5.14 (Thanks to Michael Stadler and Rick Feehery for pointing out this bug)
MethylExtract uses input BAM files without converting the entire file to SAM
MethylExtract_1.3.pl script extracts all detected SNVs (MethylExtractOutMethContexts has been included in the main script).
The memory usage has been reduced.
Default SNVs output is now VCF, check the manual or the output file header.
Default Methylation output retrieves more information and has a more compressed format.
Changed the SNVs calling (similar to varScan), giving more reliable results.
Now the chromosome IDs will be taken from the interval fasta ID (solving compatibility bugs with Bismark aligner).
Missing values in the output files will be filled up with '.' instead of '0'.
Included a script to calculate the bisulfite conversion rate from an unmethylated genome (MethylExtractBSCR_1.2.pl).
Included a script to calculate the error probability for each methylation value and assign a FDR to the entiry dataset (MethylExtractErrorProbability_1.2.pl)
Included a script to extract SNVs and Methylation ratios out of reference methylation contexts (MethylExtractOutMethContexts_1.2.pl).
Included minimum depth parameters ("minDepth").
Improved command line information and help.
Increased log-file information.
All basic functions working.
© Computational Genomics and Bioinformatics Group
Dept. of Genetics & Inst. of Biotechnology
University of Granada, Spain