Calculating alignment scores ?
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
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sunnykevin97
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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/