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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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This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.
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The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...03-03-2025, 01:39 PM -
The human gut contains trillions of microorganisms that impact digestion, immune functions, and overall health1. Despite major breakthroughs, we’re only beginning to understand the full extent of the microbiome’s influence on health and disease. Advances in next-generation sequencing and spatial biology have opened new windows into this complex environment, yet many questions remain. This article highlights two recent studies exploring how diet influences microbial...02-24-2025, 06:31 AM
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