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lh3 / minipileup

Simple pileup-based variant caller
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phasing of minipileup vcf file #11

Closed ScarlettPegany closed 3 months ago

ScarlettPegany commented 3 months ago

Hello,

Can I apply beagle or WhatsHap to phase my vcf generated using minipileup ? The goal is to determine haplotypes.

thanks !!

lh3 commented 3 months ago

I don't know. You have to try. But generally, as the README said, for typical SNP calling, GATK, deepvariant etc are more appropriate.