I'm using LoFreq software for variant calling and as the preprocessing step I'm using BaseRecalibrator/ApplyBQSR. Recently after I've updated to version 184.108.40.206 (previous was 3.5). I found that LoFreq stopped to call variants.
After some investigation I found that BAM files missing BD/BI tags. I did not find the specific release note or something that these tags are abandoned, but found an old post that developers planned to do this. Is this true that BD/BI tags are not inserted into the alignment anymore or I did something wrong?
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