Family-based filtering

[paolomaccallini-hub]

Hi!

Is there the possibility of developing a pipeline for family-based filtering of structural variants?

[lgmgeo]

Hi Paolo,

Thank you for your interesting idea!
Actually, I would really love to develop such a module (for a long time), but I know I won't have the time at the moment. I need to completely change the code and integrate a database.

Currently, I would like to add a "barcode" feature, representing the presence/absence of SV (with homozygote/heterozygote status), to search for recurrence between families or group of individuals.

The user will be able to add a list of sorted samples to the configuration file. Then, the barcode will represent the SV’s zygosity status in this ordered list of samples:

• Samples homozygotes for the reference allele will be represented using “0”
• Heterozygous SV will be represented using “1”
• Unknown SV will be represented using "2"
• Homozygous variants will be represented with “3”

(like gt_types values from the cyvcf2 Python library).

I let this issue open, so that any user interested in such a development can participate.
Feel free to expand on your needs.

Any help from developers is welcome,

Best,

Véronique