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MToolBox v.1.2
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@clody23 clody23 released this 06 Sep 15:37
· 17 commits to master since this release
v.1.2
b1d5ac5

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).

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