Update BenchmarkSVs workflow(s) with some new features #199
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kachulis
approved these changes
Feb 4, 2025
| Array[String] base_sample_names | ||
| File base_vcf | ||
| File base_vcf_index | ||
| String base_sample_name |
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so is this changing to only support benchmarking a single sample at a time?
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Yeah I wanted to keep things simpler in the WDL / Terra UI and made this just single sample for now. It would be easy to write a wrapper in the future if there was demand.
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I'll put tests on the infinite to-do list and get this merged for now. Thanks for checking! |
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This PR includes a bunch of refactoring, improvements, and new features for the process of benchmarking SV VCFs. At a high level, this includes:
truvari refineandtruvari ga4ghfor collapsing (or "harmonizing") similar events in truth/query down to one event to try to improve benchmarking statistics where calls might get mismatched due to extreme fuzziness in the calling step. This includes an alignment step usingmafftas outlined in thetruvaridocumentation on the process. The docker image is updated to include newer versions of truvari as well as mafft. This option requires the input files to be phased.