Records filtered out during realignment
some days ago, I asked for help with the BaseRecalibrator walker. One comment suggested, that the records might not be seen by the walker. Therefore I went a step back and ran the Realignment again. When I realign the records using the GATK realignment walker (first step: RealignerTargetCreator (I have overseen this the first time - I know, shame on me ;-)), the output tells me, that all reads were filtered out due to failing MappingQualityUnavailableFilter. So we have the reason, why the Recalibration fails and thank you for the suggestion.
But what goes wrong with the Realignment? Why are all records filtered out? (I mapped the reads (fastq) to hg19 with bowtie2 (default settings) and wrote the results to SAM; then performed the pipeline up to realignment).
Does anybody have an idea?