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Missing Cigar In Sam Output (Cushaw2)

Hi,

I did alignment with cushaw2, however my sam output is missing the cigar string. Is there a way to add it afterwards, or if someone is better with cushaw2, a way to tell it to add directly?

sam cigar
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updated by Biostar 380 • | written by stolarek.ir 70

the read is aligned, holds the NM and AS as the additional fields. I'm trying the fillmd with samtools, maybe this will help. Convertion to bam and viewing in igv is also working normally. I just wanted CIGAR since it's easy for me to parse it for info

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written by stolarek.ir 70

problem solved, stupid mistake

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written by stolarek.ir 70

can you add the reason as an answer? I am intrigued as to how can one one get a SAM file with no CIGAR strings

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written by Istvan Albert 10K

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