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mcveanlab / mccortex

De novo genome assembly and multisample variant calling
https://github.com/mcveanlab/mccortex/wiki
MIT License
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No reference option for bubbles/calls2vcf #63

Closed carlyprior closed 6 years ago

carlyprior commented 6 years ago

I'm struggling to figure out how to run the calls2vcf command without a reference. I see that you need a 5' flank file in SAM or BAM format, but it is unclear how I am to achieve this without a reference as both BWA and Stampy require references.

noporpoise commented 6 years ago

The VCF format requires a reference. You need some coordinate system to place variants on.

carlyprior commented 6 years ago

I see. I don't have a reference genome so is there a way to use the output from bubbles to get a VCF? Sorry for my misunderstanding about calls2vcf.

iqbal-lab commented 6 years ago

You could have a fake reference where each bubble has its own chromosome number. Assume each chromosome starts at the beginning of the flank.