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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Best way to build vcf? #490

Open vleblanc opened 4 years ago

vleblanc commented 4 years ago

Hello,

I've run CNVkit on a set of matched tumour/normal exomes and I want to get BAFs. I'd like to confirm the best approach for building an appropriate vcf file using HaplotypeCaller, since I've seen many things mentioned in various forums and issues here.

  1. Run HaplotypeCaller jointly on the normal and tumour samples. Identify tumour singletons and flag them as somatic, or maybe use Mutect2 output to flag appropriate somatic mutations.

  2. Run HaplotypeCaller on the normal sample, then calculate AF of these in the tumour sample (e.g. using the snpfilter.sh script)

Can you please confirm which (if any) is the correct approach? Thanks.

etal commented 4 years ago

If the snpfilter.sh script works on your system, then I'd recommend using that.