Whole Genome Resequencing Pipeline v2.0

Automated mapping and indel realignment of resequencing data

NEW!: SAMtools and Picard dependencies replaced by built-in MATLAB capabilities. Now only requires BWA and GATK.
Automates single-end whole genome resequence (WGRS) data processing whereby pre-installed dependencies are used to map reads from FASTQ to a reference and realign indels. BWA must be installed and available on the system path and GenomeAnalysisTK.jar must be available on the MATLAB path. If no arguments are provided, the user will be asked to provide one or more FASTQ files of reads and a reference FASTA. Developers are encouraged to adapt this template to their needs. Pipeline steps are:
(0a) FM-index reference (BWA index)
(0b) Create FASTA index (Internal fai)
(0c) Create sequence dictionary (Internal dict)
(1) Map reads (BWA mem)
(2) Convert SAM to BAM (MATLAB sam2bam)
(3) Sort BAM (MATLAB bamsort)
(4) Index BAM (MATLAB BioMap)
(5) Discover indels (GATK RealignerTargetCreator)
(6) Realign indels (GATK IndelRealigner)
(7) Cleanup