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Why intervals file have different sizes?
I ran the exact same command line twice with the exact same files and parameters and the output file is different:
gatk -T RealignerTargetCreator -nt 8 -R /home/ngs/data/tools/gatk/hg/broad_bundle_hg19_v2.2/ucsc.hg19.fasta -I $HOME/jobout/nogroupid_$JOB_ID//JFP0435_02_R2.JFP.lane5.120817FCA_sorted_remdup.bam --known /home/ngs/data/tools/gatk/hg/broad_bundle_hg19_v2.2//1000G_phase1.indels.hg19.vcf --known /home/ngs/data/tools/gatk/hg/broad_bundle_hg19_v2.2//Mills_and_1000G_gold_standard.indels.hg19.vcf --filter_mismatching_base_and_quals -o $HOME/jobout/nogroupid_$JOB_ID//JFP0435_02_R2.JFP.lane5.120817FCA_sorted_remdup.intervals
rem :Gatk vers 2.3.
Size of the intervals files are different and when I run a 'diff' it show some differences, not huge but I wonder if it's due to the algorithm:
here is the diff result: