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Interpreting "*" In Extended Cigar Format

I generated and alignment using BWA and the .sam file looks fine, except in my parser I'm not sure how to interpret the extended CIGAR format when the CIGAR string is simply "*". Looking at the samtools documentation:

http://samtools.sourceforge.net/SAMv1.pdf

It just says to the CIGAR is set to "* if unavailable", but don't really know what "unavailable" means. Should I assume the read did not align at all? What would cause BWA to produce a CIGAR of *?

samtools alignment cigar bwa
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written by anand.sarwate • anand.sarwate

1 answer

The * means no alignment to show.

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written by JC JC

Thanks -- I had seen in previous .sam files that the aligner just removed the unmapped reads, so I guess I will parse these as unmapped. If there are too many I assume I should re-run BWA with less stringent match criteria?

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written by anand.sarwate • anand.sarwate

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