PrintReads as TableRecalibration (GATK)

The TableRecalibration from GATK has been replaced by PrintReads.

The way we can use this new PrintReads is:

java -Xmx4g -jar GenomeAnalysisTK.jar 
    -T PrintReads 
    -R GRCh37.73.dna.22.fa 
    -I chr22.marked.realigned.fixed.bam 
    -BQSR recalibration_report.grp 
    -o chr22.marked.realigned.fixed.recal.bam

The file used to fill the -BQSR argument comes from BaseRecalibrator (see this previous post): recalibration_report.grp

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