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Old 10-26-2021, 12:44 AM   #1
pitch_
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Location: Singapore

Join Date: Mar 2019
Posts: 6
Default 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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gvcf, runs of homozygosity, snp calling

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