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exomiser / Exomiser

A Tool to Annotate and Prioritize Exome Variants
https://exomiser.readthedocs.io
GNU Affero General Public License v3.0
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One sample from multi-sample VCF #413

Open C-Gouveia opened 2 years ago

C-Gouveia commented 2 years ago

Hi! Is it possible to run Exomiser for one sample from a VCF with multiple samples?

I tried to run it by providing the proband ID but it errors that no pedigree file is available:

at org.monarchinitiative.exomiser.core.analysis.util.PedigreeSampleValidator.createAndValidateSingleSamplePedigree(PedigreeSampleValidator.java:90)
    at org.monarchinitiative.exomiser.core.analysis.util.PedigreeSampleValidator.validate(PedigreeSampleValidator.java:72)
    at org.monarchinitiative.exomiser.core.analysis.AbstractAnalysisRunner.run(AbstractAnalysisRunner.java:82)
    at org.monarchinitiative.exomiser.core.Exomiser.run(Exomiser.java:64)
    at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runAnalysisAndWriteResults(ExomiserCommandLineRunner.java:128)
    at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runAnalysisFromScript(ExomiserCommandLineRunner.java:124)
    at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runAnalyses(ExomiserCommandLineRunner.java:83)
    at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.run(ExomiserCommandLineRunner.java:74)
    at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:813)
    at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:797)
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:324)
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1260)
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1248)
    at org.monarchinitiative.exomiser.cli.Main.main(Main.java:44)
julesjacobsen commented 2 years ago

Sorry, no. You should be able to extract a single sample VCF using something like bcftools.