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WGS Pipeline with GATK Variant Calling

I am going to keep descriptive details of my BWA-MEM + GATK alignment and variant-calling pipeline here. This should provide a reproducible and transparent record of what we're doing. Below is an ordered list of the methods deployed in this pipeline:

1. FASTQ Splitting by Lane

• BWA_MEM Alignment
• Picard MergeSamFiles
• Picard MarkDuplicates
• GATK RealignerTargetCreator
• GATK IndelRealigner
• GATK UnifiedGenotyper
• GATK SelectVariants
• GATK DepthOfCoverage

Also, in developing this pipeline there are multiple steps that we consider, but that don't make the final cut for inclusion. A link to those pages can be found here.