Biallelic inactivation detection

Hello everyone,

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

Thanks in advance!

rna-seq genome gene

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updated 9.2 years ago by Pierre Lindenbaum

• written 9.2 years ago by Fill

1 answer

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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written 9.2 years ago by Pierre Lindenbaum

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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written 9.2 years ago by brentp

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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written 9.2 years ago by Fill

try gatk ReadBackedPhasing https://software.broadinstitute.org/gatk/gatkdocs/3.7-0/org_broadinstitute_gatk_tools_walkers_phasing_ReadBackedPhasing.php

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written 9.2 years ago by Pierre Lindenbaum

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