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lh3 / minigraph

Sequence-to-graph mapper and graph generator
https://lh3.github.io/minigraph
MIT License
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Alignment information in minigraph #70

Closed 8banzhuan closed 2 years ago

8banzhuan commented 2 years ago

Hello, I noticed that the output file after minigraph comparison is not SAM but GAF，Can GAF obtain specific mutation information like a SAM file? I checked the GAF file and it seems that there is no such information, such as information such as insertion and deletion. At the same time, I would like to ask what the characters in the last column of the GAF file mean. I searched for some information, but I didn't find any relevant introduction. For example, tp:A:P cm:i:18 s1:i:133 such characters I am looking forward to your reply, I am a beginner and I don't know much about many things, thank you

lh3 commented 2 years ago

Use option -c. It outputs CIGAR and thus substitutions and indels.