Delly and small genomes

[Pierre Lindenbaum]

Hi Tobias,

I'm trying to find a 10kb CNV in a very small genome (50kb) , (see the attached screenshot).

But delly cannot  find the CNV. I understand that there is not enough data to find the variant but do you know if there is any parameter I could change to detect this DELetion ? Or do you have any suggestion to find this kind of CNV ?

More context: I trying to find a rare SV in a large private database (human). Each time I want to download and  analyze a BAM it costs money, so I'm just downloading the reads in the region of interest and shift the positions of the reads just as if the genome was only limited to my gene of interest.

note: I'm not allowed to share the BAM data.

Thanks,

P

[Tobias Rausch]

Hi Pierre,

For the delly call subcommand, delly starts estimating the insert size distribution with 1,000 pairs, but if many of them support the deletion, it will be highly skewed. I think at >=100kbps this should work unless the breakpoints are in repeat regions.

The delly cnv subcommand really isn't intended for targeted data, I'm sorry.

Best, Tobias

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[Pierre Lindenbaum]

On Sunday, November 24, 2024 at 8:07:41 PM UTC+1 Tobias Rausch wrote:

Hi Pierre,

For the delly call subcommand, delly starts estimating the insert size distribution with 1,000 pairs, but if many of them support the deletion, it will be highly skewed. I think at >=100kbps this should work unless the breakpoints are in repeat regions.

Thanks !