Question: Calculating alignment scores ?
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gravatar for sunnykevin97
8 months ago by
sunnykevin9710
sunnykevin9710 wrote:

Hi, very new to NGS. I used most popular BWA mem for aligning Illumina pair end reads

How to calculate all these parameters for an aligned bam file ? 1) sensitivity 2) match rate and mismatch rate 3) Error rate 4) Precision and Recall

Thanks

ADD COMMENTlink written 8 months ago by sunnykevin9710

Are you after alignment stats? You could try weeSAM - it can provide stats from SAM/BAM alignment files.

More info: http://bioinformatics.cvr.ac.uk/blog/weesam-version-1-5/

ADD REPLYlink modified 8 months ago • written 8 months ago by Sej Modha4.1k
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