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  • Obtaining GVCF from bam files

    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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