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I am trying to run CountCovariates in GATK. I downloaded the most recent dbsnp file from the broad institute site. The problem is it is not sorted in chromosomal order. I have vcf-tools installed and tried to sort using the -c command. It is telling me "Obsolete version of sort command installed, please run without the -c option." But, if I type in vcf-sort -h , the usage says the -c is available. I have checked to make sure we have the most recent version. I don't find the vcf-tools website to be very helpful. Could someone point me in the right direction or do you know where I can download a sorted vcf file? Is there another program that I can use?
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The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...11-06-2024, 07:24 PM -
Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...10-18-2024, 07:11 AM
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