Calculating alignment scores ?

Question

[sunnykevin97]

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

[Sej Modha]

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/