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Old 06-29-2010, 06:31 AM   #2
Senior Member
Location: Germany

Join Date: May 2010
Posts: 101

You're right, that is somehow confusing.
By chance, I just read on the samtools manual page that samtools fillmd using option -e can "convert the read base to = if it is identical to the aligned reference base. Indel caller does not support the = bases at the moment."

I guess reporting the actual query sequence (along with the CIGAR string) makes much more sense in terms of computation because you don't need to look up the bases in the reference. And by using N, you'd lose all SNP information.
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