Biallelic inactivation detection
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5.5 years ago
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Hello everyone,

Is there any way to detect biallelic inactivation in certain genes?

Thanks in advance!

RNA-Seq genome gene • 1.4k views
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5.5 years ago
  • get a phased VCF
  • annotate the variants (SnpeFF) and filter the variants breaking the protein
  • extract the gene names for both strands
  • get the common names in both lists.
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or use bcftools csq (https://academic.oup.com/bioinformatics/article/3000373/BCFtools/csq) which can annotate the effects using phase information.

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Thank you for the answer. How to get phased VCF if I use Varscan? It it possible to get phased data from VCF after Varscan? Or I need to change my pipeline?

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