I am analysing two VCFs side-by-side for a male sample. The hard-filtered VCF (SNPs/INDELs) contains calls for chrY, whereas the CNV VCF does not contain any calls for chrY.
This was the same for a different male sample, where the hard-filtered VCF contained calls for chrY but the CNV VCF did not contain any calls for chrY.
Would you please advise?
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