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.