Question: Biallelic inactivation detection
0
gravatar for Fill
8 days ago by
Fill70
Fill70 wrote:

Hello everyone,

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

Thanks in advance!

rna-seq gene genome • 98 views
ADD COMMENTlink modified 8 days ago by Pierre Lindenbaum94k • written 8 days ago by Fill70
3
gravatar for Pierre Lindenbaum
8 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum94k wrote:
  • 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.
ADD COMMENTlink written 8 days ago by Pierre Lindenbaum94k
3

or use bcftools csq (https://academic.oup.com/bioinformatics/article/3000373/BCFtools/csq) which can annotate the effects using phase information.

ADD REPLYlink written 8 days ago by brentp22k

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?

ADD REPLYlink written 8 days ago by Fill70
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