phasing variants produced by varscan
Entering edit mode
4.8 years ago
lait ▴ 160

Hi all,

does anyone know about a tool that can phase the variants produced by varscan? I have run varscan in trio mode (for father,mother and child) and have a trio vcf file as an output.

Note: no genotype calls are present in my output trio vcf file, that is why ReadBackedPhasing didnt work for me, because it requires genotype calls, and thus I have to rerun some steps from the GATK wokflow starting from the haplotypecaller step.

gatk phasing varscan variants trio analysis • 1.2k views

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