Scripts

MTOOLBOX SCRIPTS

MToolBox.sh is the shell script invoking all the following programs:

• Sam2Fastq.jar to convert either SAM or BAM files to FASTQ format. This module is included in the ext_tools/ folder;
• mapExome.py to map reads on RSRS and hg19. It invokes GSNAP;
• SortSam.jar, MarkDuplicates.jar, SamFormatConverter.jar (PicardTools suite) for SAM/BAM manipulation at several stages of the pipeline and elimination of PCR duplicates. These modules are included in the ext_tools/ folder;
• GenomeAnalysisTK.jar (GATK suite; PMID: 20644199) for indels realignment. This module is included in the ext_tools/ folder;
• assembleMTgenome.py to assemble the mitochondrial genome and perform variant calling and heteroplasmy quantification, by invoking:
  • mpileup (samtools)
  • mtVariantCaller.py module;
  • VCFoutput.py to report variants in the VCF file (version 4.0). It invokes the vcf module (PyVCF release 0.60);
  • mt-classifier.py for haplogroup prediction;
  • variants_functional_annotation.py for functional annotation;
  • prioritization.py for variant prioritization;
  • summary.py to report statistics about coverage of reconstructed genomes, predicted haplogroups, number of homoplasmic, heteroplasmic and prioritized variants.