VQSR and sex chromosomes

tiagoantaotiagoantao Posts: 1Member


Maybe I have not been able to find some obvious piece of documentation, but I am searching for best practices in using VQSR with sex chromosomes (especially X)? I am trying to do variant calling on Anopheles gambiae genomes (sex chromosomes like human) and the results with chromosome X are not very encouraging. I was wondering if there is any documentation/best practices for VQSR with especially X. Or even if people are using VQSR with sex chromosomes?

Clueless and lost, Tiago


  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,929Administrator, GATK Developer admin

    Hi Tiago,

    We do not have any specific recommendations for sex chromosomes, largely because we don't do anything with them ourselves. In humans at least X and Y are notoriously difficult to call because the mapping of reads there is typically of very poor quality. And since VQSR relies on large numbers of observations to do its job, it can't deal very well with localized aberrations such as those that might affect the sex chromosomes. So if the situation is similar in Anopheles, then unfortunately you may be in for a rough ride. Perhaps someone in the community might have more experience dealing with this problem and will share their approach...

    Geraldine Van der Auwera, PhD

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