monarch-initiative / pheval

A framework for empirical evaluation of phenotype matching and prioritisation
https://monarch-initiative.github.io/pheval/
Apache License 2.0
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317 add arguments hg19 vcf dir and hg38 vcf dir to spike vcf command #322

Closed yaseminbridges closed 5 months ago

yaseminbridges commented 6 months ago

Add arguments for specifying a directory of hg19 or hg38 VCFs to spike variants in for the spike VCFs command.

No changes to code structure - just now adding the option to iterate through a directory of VCFs and select one at random for each phenopacket to spike the variant in. This should help with problems in benchmarking with the same background VCF for all samples