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Why intervals file have different sizes?

didiercroesdidiercroes Member Posts: 4
edited July 2013 in Ask the GATK team

Hi,
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

Didier

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,428 admin

    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.

    Geraldine Van der Auwera, PhD

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