-L option
Posted in Ask the GATK team | Last updated on 2013-02-20 03:07:11


Comments (1)

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.


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