Dear all,
My aim is to identify Runs of Homozygosity(ROH) in my samples. I kept getting 0 ROHs in both Plink and detectRUNs softwares from ANGSD output. I assume this is because the tped files I have obtained from ANGSD (-doplink 2) does not include the homozygous regions. As such I would need a program that can generate a GVCF to get ROH.
Currently, I have only found GATK (-ERC GVCF) to generate a GVCF. However it is taking very long on my whole genome data, it has been running for almost 5 days and it's only at chromosome 3. I am wondering if my thought process is correct and if anyone knows speedier methods to get a GVCF?
Many thanks!
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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