Commits

Author Commit Message Labels Comments Date
arodri7
Fixing GATK flagstat nt option
arodri7
adding GATK3 Flagstat
arodri7
updated to the isaac illumina based tools
arodri7
adding null values to WGSMetrics tool
arodri7
gatk3 reference updates
arodri7
updating the tools config files
arodri7
adding picard_CollectQualityYieldMetrics.xml
arodri7
adding parameters to the gatk tools
arodri7
adjusting tool to version 1.129 picard
arodri7
Adding collectWGS changes to the python wrapper
arodri7
updating the fasta locations file
arodri7
updating fasta locations file
arodri7
setting heap size
arodri7
fixing the flags for read group
arodri7
adding batch friendly bwamem
arodri7
optimizations to bwa_mem
arodri7
adding gatk3_SplitNCigarReads utility
arodri7
additonal optimization to bwa-mem wrapper
arodri7
update picard wrapper to accept the tool name
arodri7
commenting out reference genome filter option
arodri7
fixing issue for sorting large size datasets
arodri7
optimizations to bwa-mem to print out a sorted BAM file
arodri7
correctly filling out bam format parameter
arodri7
fixing jar path on the python script for picard wrappers
arodri7
adding wrappers for new version of picard tools
arodri7
updating location of reference files
arodri7
making samtools current version the default and fixing bam output format request
arodri7
fix additon to library in bcl2fastq wrapper
arodri7
fixing PATH env for bcl2fastq
arodri7
fix bug for bcl2fastq
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