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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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...07-08-2024, 03:19 PM