Question

Biallelic inactivation detection

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7.5 years ago

Fill ▴ 70

Hello everyone,

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

Thanks in advance!

RNA-Seq genome gene • 1.8k views

ADD COMMENT • link updated 7.5 years ago by Pierre Lindenbaum 164k • written 7.5 years ago by Fill ▴ 70

score 3 · Accepted Answer · 2017-06-13

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7.5 years ago

Pierre Lindenbaum 164k

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 COMMENT • link 7.5 years ago by Pierre Lindenbaum 164k

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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.

ADD REPLY • link 7.5 years ago by brentp 24k

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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?

ADD REPLY • link 7.5 years ago by Fill ▴ 70

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

ADD REPLY • link 7.5 years ago by Pierre Lindenbaum 164k