Hello everyone!
I'm working with the WES data of a family with hypothyroidism and deafness with an apparently AD inheritance; our group haven't had identified the genes involved in the developing of this illnes, so, we are interested in investigating the consanguineous state of the patients in order to have more information to analyze this case.
I'm a beginner in this kind of studies, so if you have some tips on how to infer the possible consanguinity status of the patients I will very appreciate your contributions .
Hi Eduardo Bernal Barquero
Google Brain Team recently released DeepVariant which you can use as an alternative to GATK.
We implemented a reproducible version that was submitted to NF-Core (https://lifebit.page.link/UW58).
We also made it available in Lifebit (https://lifebit.page.link/os1m) if you want to try it with example parameters.
In practice, DeepVariant first builds images based on the BAM file, then it uses a DeepLearning image recognition approach to obtain the variants and eventually it converts the output of the prediction in the standard VCF format.
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