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  • Where is alignment score when using bwa aln and sampe commands are used ?

    I used bwa aln and bwa sampe commands. But in the output I can't find AS tag.

    It seems AS tag is reported by bwasw and is long-red specific, according to https://sourceforge.net/p/bio-bwa/ma...sage/27302475/. bwa aln and bwa sampe will not produce AS tag in the output.

    If I want to do some filter based on alignment score with the output from bwa aln and bwa sampe, what am I supposed to do ?

    Thanks a lot for sharing you ideas.

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