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-L option

genaro_pimientagenaro_pimienta Member Posts: 15
edited February 2013 in Ask the GATK team

Hello,
I want to know how important it is to have the -L target-intervals.intervals option in UnifiedGenotyper, and if it is recommended in VariantCallRecalibrator too.

I have ran the Unified Genotyper tool with 1 input file at a time or the 2 files I want to compare at once.
My command-lines are the following:

java -jar -Xmx15g GenomeAnalysisTK.jar -R ./genome.fa -T UnifiedGenotyper -I ./1.bam --dbsnp ./dbsnp_137.hg19.vcf -o ./1-gatk.vcf  --min_base_quality_score 25 -stand_call_conf 50 -stand_emit_conf 10 -dcov 200 -L ./intervals-1.intervals

java -jar -Xmx15g GenomeAnalysisTK.jar -R ./genome.fa -T UnifiedGenotyper -I ./2.bam --dbsnp ./dbsnp_137.hg19.vcf -o ./2-gatk.vcf  --min_base_quality_score 25 -stand_call_conf 50 -stand_emit_conf 10 -dcov 200 -L ./intervals-2.intervals

java -jar -Xmx15g GenomeAnalysisTK.jar -R ./genome.fa -T UnifiedGenotyper -I ./1.bam -I ./2.bam --dbsnp ./dbsnp_137.hg19.vcf -o ./1vs2-gatk.vcf  --min_base_quality_score 25 -stand_call_conf 50 -stand_emit_conf 10 -dcov 200 -L ./intervals-1.intervals -L ./intervals-2.intervals

Thanks,
G.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,413 admin

    It depends on your experimental design and dataset. Assuming you are working with exome data, all the steps are going to run faster if you run with -L target_intervals because the tools won't bother looking at the areas outside those intervals, which shouldn't be covered anyway.

    If your bam files use the same intervals, you can pass them together. If not, then it may be better to process them separately. FYI if you pass two intervals file, the GATK engine will take the union of the two sets, merging any overlapping intervals.

    Geraldine Van der Auwera, PhD

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