BI and BD tags.
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?
Looks like BI BD tags are deprecated with gatk 4.0 as HC does not rely on them anymore. If you wish to continue with older gatk versions or software that relies on BI BD tags then you need to perform BQSR using GATK 3 releases.
That was my thought. Thanks!
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