Mismatch and Indel rate in alignment
I am using BWA to align the raw reads against a contig set. I would like to know the overall mismatch rate as well as indels in the entire alignment (SAM/BAM). I tried various options of samtools/bamtools, but could not able to find this.
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BDK_compbio
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check this out Mismatch and Indel statistics from BAM/SAM file
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