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yatisht / usher

Ultrafast Sample Placement on Existing Trees
MIT License
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Ancestral node VCFs #291

Closed lenorakepler closed 1 year ago

lenorakepler commented 1 year ago

Hi there,

Thank you all so much for such a great tool!

I was wondering if it is currently possible to output a VCF file of the "genotypes" of the ancestral nodes in a MAT, as is already done for the tips with the matUtils extract --write-vcf option.

Thanks! Lenora Kepler

yatisht commented 1 year ago

This is already possible if you provide the internal node ids in the MAT instead of tip names. For e.g.

matUtils extract -s samples.txt -i in.pb -v out.vcf

Where samples.txt could contain a list of internal node labels:

node_6
node_25

Is this what you're looking for?

-Yatish

lenorakepler commented 1 year ago

That is exactly what I was looking for, thanks so much!