MToolBox v.1.2.1

Fix to heteroplasmy calculation of insertions and deletions that previously returned underestimated values.

MToolBox v.1.2

Update to MToolBox v.1.2

1. A bug in consensus fasta sequence generation has been fixed. The bug caused heteroplasmic variants to be included in the consensus fasta sequence (generating many IUPAC ambiguity and incorrect haplogroup predictions).

2. Changes in the mapExome.py to remove reads that show a number of soft-clipped bases > 1/3 read length. This is to remove reads that show unique best alignments to mtDNA but still carry a small portion of the non-aligned read that can putatively map on nuclear homologous (NumtS) sequences.

3. Strand-specific read depth has been added as a new feature to the VCF, under the new field SDP. This field reports the number of forward and reverse reads supporting the alternative allele, expressed as F;R, where F is the number of forward reads and R is the number of reverse reads.

4. Additional options can be now specified in the configuration file (or default values will be considered).

MToolBox.v1.1

• Fix of the phylotree build 17 tree parsing, causing replacement of haplogroups.txt and phylotree_r17.pickle files. The bug was causing wrong predictions mostly for X haplogroups.

• Fix in the mtVariantCaller.py causing issues #64 and #72

• Fix in the MToolBox.sh causing failing with multiple haplogroup predictions (issue #73 ). Credits to @psterk.

MToolBox

MToolBox v.1.0 is installed by the install.sh script and relies upon the following dependencies:

• Python 2.7 (www.python.org, provided within the Anaconda distribution, https://www.continuum.io/downloads)
• GSNAP (http://research-pub.gene.com/gmap/)
• Samtools (https://sourceforge.net/projects/samtools/files/samtools/)
• MUSCLE (http://www.drive5.com/muscle/downloads.htm)
• ZLIB (http://zlib.net/)
• Picard tools (https://broadinstitute.github.io/picard/command-line-overview.html)

MToolBox

Previous version of MToolBox, without the install.sh.