Hello,
we have performed a WES of a single human sample and I am interested to analyse the runs of homozygosity in this sample. Especially, I am interested to unterstand if segmental uniparental isodisomy or parental relatedness is the cause for a large homozygous region in this sample. Unfortunately, we do not have DNA of the parents.
Therefore, I need bioinformatic support and would be happy about a cooperation. Please feel free to contact me.
Thanks Andreas
I can look into the data if you need help in terms of data processing.
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.
- Badges
- Science topic
- Similar topics
- Biological Science
- Kinesiology
- Running