Comparing variants in family trios in Python

Question

[MediumHeat]

Hello guys! Im pretty new into Bioinformatics and have some questions about it. Im currently working with a VCF-File with more than 1 Person in it (Mother,Father,Child) in Python. My problem right now is that i have the allels from everyone in the file but when you are looking at the childs allels i need to tell the user which allel comes from the mother and which from the father or none. I would be very thankful if someone could give me some hints to do this in Python and help me finishing the task.

I thank you in advance for your help

Stay safe!

Answer 1

[brunobsouzaa]

Don´t know in Python but you can use vcf-isec for this task. It´s pretty easy to use and you can intersect the child´s vcf with each parent and get the output for each intersection!

Hope it helps.

Answer 2

[mikpom]

I was recently developing a Python package genomvar to work with genomic variants in Python data analysis ecosystem.

It is rather new but maybe you find it of use.