== GATK ==

=== VariantAnnotator ===

{{{
java -jar /usr/local/GATK/GenomeAnalysisTK.jar -T VariantAnnotator -R /data/CCRBioinfo/public/GATK/bundle/1.5/hg19/ucsc.hg19.fasta -I AS_DNA_Normal.recal.md.realigned.bam -I AS_DNA_Tumor.recal.md.realigned.bam -V tmp.vcf -U -o tmp.gatk.vcf -A AlleleBalanceBySample -A MappingQualityZeroBySample -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A BaseQualityRankSumTest -A HaplotypeScore -A RMSMappingQuality -A LowMQ -A HomopolymerRun -A BaseCounts
}}}