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Use GVCFs for genotyping - run time/CPU hours substantially reduced (0.52) #158

Merged
merged 16 commits into from
Jun 7, 2024
Merged

Use GVCFs for genotyping - run time/CPU hours substantially reduced (0.52) #158

merged 16 commits into from
Jun 7, 2024

Commits on Mar 29, 2024

  1. use F72 config for F16

    @sorelfitzgibbon
    sorelfitzgibbon committed Mar 29, 2024
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Commits on Mar 30, 2024

  1. add genotype from gvcfs

    @sorelfitzgibbon
    sorelfitzgibbon committed Mar 30, 2024
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  2. tmp F16 changed to F72 values

    @sorelfitzgibbon
    sorelfitzgibbon committed Mar 30, 2024
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Commits on Mar 31, 2024

  1. add combine and genotype gvcfs

    @sorelfitzgibbon
    sorelfitzgibbon committed Mar 31, 2024
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  2. tmp F72 to F16 config

    @sorelfitzgibbon
    sorelfitzgibbon committed Mar 31, 2024
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Commits on Apr 1, 2024

  1. tidy up scripts and replace input validation

    @sorelfitzgibbon
    sorelfitzgibbon committed Apr 1, 2024
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  2. replace original F16.config

    @sorelfitzgibbon
    sorelfitzgibbon committed Apr 1, 2024
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  3. update changelog

    @sorelfitzgibbon
    sorelfitzgibbon committed Apr 1, 2024
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Commits on Apr 2, 2024

  1. update gatk

    @sorelfitzgibbon
    sorelfitzgibbon committed Apr 2, 2024
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  2. update resources

    @sorelfitzgibbon
    sorelfitzgibbon committed Apr 2, 2024
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Commits on Apr 3, 2024

  1. removed unused genomicsdb-import

    @sorelfitzgibbon
    sorelfitzgibbon committed Apr 3, 2024
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  2. fix intermediate output

    @sorelfitzgibbon
    sorelfitzgibbon committed Apr 3, 2024
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  3. adjust resources

    @sorelfitzgibbon
    sorelfitzgibbon committed Apr 3, 2024
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Commits on May 10, 2024

  1. update changelog

    @sorelfitzgibbon
    sorelfitzgibbon committed May 10, 2024
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Commits on May 31, 2024

  1. remove intervals from combine-gvcfs

    @sorelfitzgibbon
    sorelfitzgibbon committed May 31, 2024
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  2. remove unused haplotypecallervcf

    @sorelfitzgibbon
    sorelfitzgibbon committed May 31, 2024
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