Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.



Last Active


  • @Sheila I am not sure what you mean. It is currently not in number order. VCF sort says it sorts according to the contigs in the header which is what it is like now - non numerical order, it has chromosome x between 7 and 8 and chromosome 19 after …
    in GVCF Sort Comment by TamaraP April 2018
  • Hi @Geraldine_VdAuwera would you be able to comment on the issue raised above. I am having a very hard time trusting the output of any of the homozygosity tools as they are all so different and not conclusive. I also doubt that the largest ROH in t…
  • @SkyWarrior thanks so much for your insights. I will try what you suggested! Let me know when the tool you are developing for your thesis is out, I would love to give it a try as well.
  • @SkyWarrior Yes I am working on WES data. I have been trying to work with HomSI for quite a while but I didnt get any long runs of homozygosity. It was really difficult to say if there was any region of interest at all on this patient. There was alw…
  • @SkyWarrior I originally tried using HomSI and Homozygosity Mapper with the VCF files I had, but there were a lot of no call regions which I could not figure out how to resolve. I thought the GVCF may reolve that issue, by providing the missing geno…
  • Hi, I was looking at this post to see if it can guide me in the right direction. I generated GVCF files using BAM files. I would like to analyze this individual for homozygous regions in order to decide whether to prioritize homozygous or compound …