Added FastQC to software tools section.
FastQC script for QC of fastq files; input is a file containing a list of files (full paths) to be QCed. Job runs as array job, one job per line of the input file.
Removed multi-threading and added flag to prevent extraction of compressed output
Added directory containing ANNOVAR perls and databases
Changed location of global setting files in ExmRes.2.bwa_index_reference.sh
Added resources and allocations for ANNOVAR scripts
Added call annotation scripts to ExmVC.4
Some minor fixes.
Added script to download databases for ANNOVAR
VCF header file for use with ANNOVAR
First drafts of scripts to add Stampy into the pipeline.
AlignStampy - does alignment from BAM that has already been aligned with BWA mem, skips read with good BWA mem alignments
ConvSamtoBam & ConvSamtoBamandDedup - Stampy outputs in SAM format, convert back to BAM
First drafts of scripts for annotation of VCF with ANNOVAR