Minor updates to BQSR for GATK 2.0
Switches to gatk 2.0 beta
Removes some steps no longer needed for the gatk 2.0
Adds by chr data store to spead up huge lists
Adds :trim_end opt to runs/sequence
Updates for gatk 2
Changes compression level for intermediate bam
Moves to 2.2-13-gab9f9b3 gatk. Chagnes to nct nanoscheduler multithreading
Mering in from master
Merge branch 'gatk_2.0' of /Users/glennsb/omrf/src/ngs_scripts into gatk_2.0
Changes compression levels on imtermediate BAM files
Changes bwa to version 0.6.2
Adds ngs.q to scatter & gathered calling
Removes AlleleBalance annotation with Haplo based caller
Merge commit '45cc76f' into gatk_2.0
Merge commit '98b0846' into gatk_2.0
Fixes bug of removing input fastq if skip btang
Fixes bug of removing input fastq if skip btang
Adds option to skip_indel_realign
Merges in master for skip_indel_realign option