It looks like you're new here. If you want to get involved, click one of these buttons!
Hi all; I use the old version of GATK and it seems that -T TableRecalibration does not work correctly on my .bam file. Nothing is printed out as BQ tag although I use these parameters:
java -Xms5g -Xmx5g -jar $GATK/GenomeAnalysisTK.jar \ -R $REF \ -I $d/$f\_marked.bam \ -o $d/$f\_recalibrated.bam \ -T TableRecalibration \ -baq RECALCULATE \ --doNotWriteOriginalQuals \ -recalFile $d/$f\_marked.bam.csv \ -et NO_ET
I would appreciate any input.