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it turned out I had to set Downsampling to None. My AD and DP were under reported due to the downsampling. -
GATK reported AD and DP
I am using Unified Genotyper for SNP calling. I find that the reported Allele depths and read depths seem much lower than expected (with and without the base quality recalibration). I did the alignment using CLC bio and have a SNP file from CLC bio which reports the coverage at the SNP position of reads that passed the quality filter. I understand the reported coverage values may not be exact but for equivalent quality scores, I find the DP from GATK to be 10% or 20% of the CLC bio coverage. Has anyone else seen this? Does GATK scale down the coverage?
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Metagenomics has improved the way researchers study microorganisms across diverse environments. Historically, studying microorganisms relied on culturing them in the lab, a method that limits the investigation of many species since most are unculturable1. Metagenomics overcomes these issues by allowing the study of microorganisms regardless of their ability to be cultured or the environments they inhabit. Over time, the field has evolved, especially with the advent...09-23-2024, 06:35 AM -
During the COVID-19 pandemic, scientists observed that while some individuals experienced severe illness when infected with SARS-CoV-2, others were barely affected. These disparities left researchers and clinicians wondering what causes the wide variations in response to viral infections and what role genetics plays.
Jean-Laurent Casanova, M.D., Ph.D., Professor at Rockefeller University, is a leading expert in this crossover between genetics and infectious...09-09-2024, 10:59 AM
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