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Hi,

If I take an aligned BAM, run samtools reset | samtools fastq -T \* to get a fastq-file, align that file to a different reference genome with minimap2 -y to copy fastq-tags over to the output, I'm worried that IGV will display these as wrongly split alignments, when the SA-tag is copied to the aligned-BAM?

I'm not sure if I'm missing something here, why is the SA-tag kept in samtools reset by default?

Thanks!