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 complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...07-08-2024, 03:19 PM