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-L Argument in WES
I am performing the whole exome sequencing analysis and pretty confused with the -L option in GATK walkers. Is it necessary to provide the regions.bed file in the -L option during the first step of Realignment. In my command line I am using the -known sites. Will that be not sufficient to allow the local indel realignment in small datasets like exomes.
My command line is as follows:
java -jar -Xmx4g GenomeAnalysisTK.jar -T RealignerTargetCreator -I .bam -R hg19.fa -known Mills_and_1000G_gold_standard.indels.b37.vcf -o .realign.intervals