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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