realignIndelsGATK: Realign indels via GATK
Description
Realing indels using the GATK tools RealignerTargetCreator
and IndelRealigner.
Requires a GATK compatible genome with a name matching
the alignment genome to be installed in 'path.gatk_genome'
Usage
realignIndelsGATK(bam.file)
Value
Path to realigned bam file
Details
Since GATKs IndelRealigner is not parallelized, we run it in
parallel per chromosome.