detecting deletions in chromosome Y

[Subin Choi]

Hi,

I am new to using the SV caller and aiming to detect a deletion in a specific region in chromosome Y with Delly.

I have got germline WGS data (~ 23.5X and low-coverage) which I have extracted chrY regions only. I have a deletion (>2Mb long) which is normally detected by using sequence-tag-sites(STSs) in PCR.

My assumption is if i could detect deletions in these STS regions using DELLY, I can find the samples with the deletions of my interest. 

Could you give me advice on which function and options of DELLY I could use to optimise this?  I think detecting hemizygous variant might need some treaking in running methods or interpreting the results.

 

Thank you!

Subin

[Subin Choi]

Hi - I have updated my method and now trying to use delly's Germline CNV calling. Again, i only have WGS data in chrY region. I keep getting an error 'Not enough windows'. Could you tell me what this means and how I can go about to fix it?

Thank you.

Subin

[Tobias Rausch]

Hi Subin,

I don't have much experience with chrY but you probably want to use the T2T assembly for chrY and not hg38. In addition, it's better to keep the BAMs as they are and not to subset them to chrY.

Best, Tobias

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[Subin Choi]

Hi Tobias,

Thank you for the response.

Regarding 'Not enough windows' error, is this due to the subsetted bam file?

Thank you!

Subin