Question: Biallelic inactivation detection
0
gravatar for Fill
7 months 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 • 332 views
ADD COMMENTlink modified 7 months ago by Pierre Lindenbaum103k • written 7 months ago by Fill70
3
gravatar for Pierre Lindenbaum
7 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum103k 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 7 months ago by Pierre Lindenbaum103k
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 7 months 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 7 months ago by Fill70
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1376 users visited in the last hour