I ran the following code:
java -Xmx100g -jar /work/reecygroup/GATK/GenomeAnalysisTK.jar \
-T BaseRecalibrator --unsafe -nct 16 \
-R /work/reecygroup/index/bos_taurus/bos_taurus_all_dna.fa \
-I 2005-5105.realigned.bam \
-knownSites /work/reecygroup/christine/Bos_taurus.dbSNP.vcf \
-o 2005-5105.realigned.grp \
--fix_misencoded_quality_scores
and got the error:
Bad input: while fixing mis-encoded base qualities we encountered a read that was correctly encoded; we cannot handle such a mixture of reads so unfortunately the BAM must be fixed with some other tool
The "index" and "knownSites" files have been successfully used in other run for quite some time, and the input BAM file (2005-5105.realigned.bam) was generated with a previous GATK IndelRealigner step. I wonder what could be wrong and what I need to do in order to fix it?