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  • Dendrobium--
    started a topic Count error rate of sam file

    Count error rate of sam file

    I have aligned the fastq file to the reference genome and got a sam file. I know use "samtools stats" can get "error rate" of the sam file.

    Is there any document shows how the error rate is calculated from the sam file? (since I want to seperately calculate the error rate of every read in the sam file instead of the average of the whole file)

    Meanwhile,is there any easy way to combine the CIGAR and MD strings to to get the insertion,indel and mismatch base of each read aligned to the reference genome.

    Any answer is appreciated.

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    Multiomics Techniques Advancing Disease Research
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    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

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