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changelog.md

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###CHANGELOG - 5 June 2014

  • changed the method for estimation of the heteroplasmy confidence interval (CI). For sites with coverage depth <= 40, the heteroplasmy CI is estimated with the Wilson score interval; for larger coverage depth values, the Agresti-Coull interval is used.
  • added the possibility to use fasta inputs to perform haplogroup prediction and functional annotation.
  • added the possibility to use the revised Cambridge Reference Sequence (rCRS) as reference sequence for read mapping. By using rCRS as reference sequence, the VCF output will be rCRS-based.

###CHANGELOG - 19 July 2014

  • an error encountered during the bam to fastq extraction has been fixed. Empty unpaired fastq files are now removed.

###CHANGELOG - 29 September 2014

  • an error fixed in the -t parameter of assembleMTgenome.

###CHANGELOG - 6 November 2014

Update to MToolBox version 0.2.1:

  • an error encountered during the sam to fastq extraction has been fixed in the MToolBox.sh file.
  • RCRS, hg19RCRS, RSRS and hg19RSRS gmap indexed databases have been regenerated using the -c option for circularized chromosomes.
  • update to Phylotree Build 16 for haplogroup prediction.

###CHANGELOG - 23 January 2015

Update to MToolBox version 0.2.2:

-an error encountered during the analysis of hard clipping mapped reads has been fixed in the mtVariantCaller.py -the mtVariantCaller.py has been improved to better manage sites with multiple alleles. -hidden files included in the package and generating problems with the mt-classifier.py have been eliminated.

###CHANGELOG - 25 February 2015

-An error occurred during the generation of circularized mitochondrial chromosome, used for the gsnap db generation. Hg19RCRS/hg19RSRS and chrRCRS/chrRSRS gsnap indexed databases have been replaced with those using the linearized mitochondrial chromosome. We apologize with the MToolBox users for this inconvenient.

###CHANGELOG - 28 February 2015

Update to MToolBox version 0.3 with the following new options and changes:

  • fastq.gz is a further possible input format file. Installation of zlib libraries is therefore required.
  • users can specify the path of the working directories using –p (path to input folder) and –o (path to output folder) options.
  • users can specify a list of files to be used as input through -l option. It accepts a text file containing one sample name for each line. This list should be named as "list.txt" and placed in the input folder. Alternatively, users can provide comma-separated names with the same option. It is mandatory to report in such list the filename extension (e.g. mysample.sam or mysample.R1.fastq).
  • users can use -X option to allow the extraction from a BAM file of mitochondrial reads mapped onto a mitochondrial reference sequence. This option can be useful when using Whole Genome or Exome sequencing BAM files containing a huge amount ofnuclear reads. The option works only with the BAM format.

new fields added to the annotation.csv output file:

  • Disease Score: "% Disease", "% Neutral" and "% Unclassified" fields have been replaced with an overall Disease Score, generated as a weighted average of pathogenicity prediction scores for non-synonymous variants, derived from a training dataset of 53 non synonymous variants selected among mitochondrial diseases or cancer associated mutations. Weights have been calculated by taking into account the right prediction and the best probability to predict a truly pathogenic mtDNA variants generated by the pathogenicity prediction algorithms currently implemented in MToolBox.
  • MutPred Pred: MutPred prediction (Low pathogenicity, High pathogenicity).
  • dbSNP ID: Variant ID in dbSNP.

for users convenience, new scripts to help the generation of reports about the annotated and prioritized variants have been added to the suite of tools provided by MToolBox:

  • prioritization.py, which generates the prioritized_variants.txt file, reporting annotation only for prioritized variants for each sample analyzed, defined as variants recognized by the three reference sequences (rCRS, RSRS and MHCS), sorted per increasing variability.
  • summary.py, which generates the summary.txt file, reporting statistics about the coverage of reconstructed mitochondrial genomes, number of homoplasmic and heteroplasmic variants (for NGS data), haplogroup prediction and number of prioritized variants.

###CHANGELOG - 8 June 2015

Update to MToolBox version 0.3.1 with the following change:

  • A bug in the MToolBox.sh script has been fixed. Empty paired-end fastq files generated during SAM/BAM to fastq conversion are now removed.