I tried to use mpileup in samtools to call SNP and indel from 200 individuals of whole genome sequencing. However, it is a time consuming job, in about 10 days, only the variants in three chromosomes have been outputted in the bcf file. So, if the mpileup can make variants call separately in chromosomes, I can run multiple chromosomes at the same time on my computer. But the parameter -l need the user to provide candidate variants position.Does anyone have some experence in this situation?
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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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