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-L option with PrintReads
I am using GATK-3.6 to analyze exome sequencing data. To speed up the analysis I split the BED file provided in GATK resource bundle (Broad.human.exome.b37.bed) into several files, one for each chromosome. I created the BQSR tables separately (in parallel) for each chromosome using the -L option. Under theses circumstances can I use the -L option with PrintReads to run on each BQSR table separately as well. It is not recommended in http://gatkforums.broadinstitute.org/gatk/discussion/4133/when-should-i-use-l-to-pass-in-a-list-of-intervals. The input to PrintReads file is a single deduplicated BAM file. Indel realignment is not performed