lgmgeo
commented
11 months ago 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
Hi!
Is there the possibility of developing a pipeline for family-based filtering of structural variants?