Is there any way to detect biallelic inactivation in certain genes?
Thanks in advance!
or use bcftools csq (https://academic.oup.com/bioinformatics/article/3000373/BCFtools/csq) which can annotate the effects using phase information.
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?
try gatk ReadBackedPhasing https://software.broadinstitute.org/gatk/gatkdocs/3.7-0/org_broadinstitute_gatk_tools_walkers_phasing_ReadBackedPhasing.php