To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

Why intervals file have different sizes?

didiercroesdidiercroes Member
edited July 2013 in Ask the GATK team

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:

158138c158138 < chr2:905714-905956 --- > chr2:905685-905956 452144c452144 < chr3:195511953-195512064 --- > chr3:195511916-195512064 461418c461418 < chr4:9241955-9242059 --- > chr4:9241966-9242059 605566,605567c605566,605569 < chr5:21481723-21482150 < chr5:21482294-21482726 --- > chr5:21481723-21481740 > chr5:21481909-21482150 > chr5:21482294-21482563 > chr5:21482690-21482726 605569c605571,605573 < chr5:21484233-21484258 --- > chr5:21483481-21483649 > chr5:21483821-21484114 > chr5:21484233-21484265 615246c615250 < chr5:34189680-34190048 --- > chr5:34189714-34190048 615248a615253 > chr5:34191846-34192088 909440,909441c909445 < chr7:100643452-100643460 < chr7:100643595-100643794 --- > chr7:100643452-100643794 1008760c1008764 < chr8:86572070-86572117 --- > chr8:86572070-86572085 1008763c1008767 < chr8:86573453-86573764 --- > chr8:86573453-86573707 1478683c1478687 < chr14:19553519-19553562 --- > chr14:19553519-19553559 1478828c1478832 < chr14:20019712-20019990 --- > chr14:20019712-20019951 1994633c1994637 < chrUn_gl000212:6736-6842 --- > chrUn_gl000212:6736-6843

Kind regards



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Didier,

    That's probably due to multithreading. Between runs, different reads will be taken into account to determine the boundaries of the intervals. This shouldn't be a cause for concern.

Sign In or Register to comment.