ChrY

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LG

• November 17, 2023 15:38

Hi,

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?

Thank you.

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  Gökalp Çelik

  • November 17, 2023 19:50

  Hi LG

  Did you create these VCF files yourself or did you get them from elsewhere (Service provider, colleague etc.)? Were you expecting you see a particular CNV event in chrY? Were those VCFs generated by GATK tools? 

  The way CNVs are called is usually quite different from short variants therefore it may be possible that chrY could have been omitted from the analysis of CNVs so you don't observe anything. 

  If you can provide us more details we may be able to help. 

  Regards. 

   

   

   

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  LG

  • November 17, 2023 20:34

  Hi Gökalp,

  Thank you for your response. I received the files from a colleague, who had run Illumina’s DRAGEN pipeline on the samples. I am not totally clear about this — but it seems like GATK and DRAGEN at some point ‘fused’ their technologies? The data I am analysing was generated in 2021.

  I wasn’t expecting to see any particular CNVs on the Y chromosome, but given that there were CNVs on the other chromosomes for both male patients, including the X chromosome, I figured there must be a few for the Y chromosome (even if it would only be a few because the Y chromosome is small).

  I had originally looked into this because the merged segmentation files didn’t show any Y chromosomal hits for either male sample, despite the segmentation file also showing copy neutral chromosomal coordinates for the other chromosomes.

  Would you please advise?

  Thank you.

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  Gökalp Çelik

  • November 17, 2023 22:33

  GATK and DRAGEN share certain common algorithms and technologies however CNV analysis of DRAGEN is still on its own therefore we do not have any DRAGEN equivalent CNV tool but our own. You may need to check with your colleague to see how CNV analysis works on DRAGEN therefore you will get an idea why you do not observe any CNV events on chrY. 

  Unless these CNV VCFs are created by GATK Germline CNV calling workflows we may not be able to tell how this is happening other than guessing that this might be due to extreme filtering of regions or masking Y chromosome multimapping regions. 

  I hope this helps.

   

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