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alexdobin / STAR

RNA-seq aligner
MIT License
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CIGAR X and = instead of M #2088

Open ggPeti opened 3 months ago

ggPeti commented 3 months ago

Hello,

I can't seem to find a way to make STAR output X and = in CIGAR string, only M. Yet, some comments online seem to hint at the possibility of this.

Am I missing something? Please inform me.

Thank you!

ghuls commented 3 months ago

You can always use:

samtools calmd -e -o aln.with_X.bam aln.bam ref.fasta