I am working on amplicon data from an aploid genome (same length, already aligned with a miltiple alignment). Since I cannot generate a .bam file I've to call mutations from aligned fastq through base count generation. To validate a mutation I've to calculate genotype likelihood, but I cannot find a simplified version of the formula, despite I found a 'simpler' formula that expoites counter for GL calculation (https://gwct.github.io/referee/calcs.html). Moreover, all these formulae are not well explained in the page, so I am wondering if someone has already tryed to calculate GL by hand ( having base counts, base qualities and mapping qualities). If possible, I would like to calculate GL in a 'samtools like' manner which is more conservative respect GATK and other tools
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The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
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The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
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