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Sheryl

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Latest activity by Sheryl
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    Sheryl created a post,

    Workflow for WES/WGS

    1. Community
    2. New User Advice

    I have used ExomeGermlineSingleSample_v3.1.9 wdl to create gVCFS. Please can you confirm that I now need to consolidate the vcfs using GenomicsDBImport, joint genotype using GenotypeGVCFs and filte...

    • Sheryl
    • 2 followers
    • 1 comment
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    Sheryl commented,

    1. Community
    2. New User Advice
    3. cnv_germline_case_workflow.wdl

    So are you saying that unless you have >30 samples you can't do CNV calling at all? If I have 30 samples, do I have to use DetermineGermlineContigPloidyCohortMode beforehand to generate the require...

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    Sheryl created a post,

    cnv_germline_case_workflow.wdl

    1. Community
    2. New User Advice

    I'm trying to get started using the cnv_germline_case_workflow.wdl from here: https://github.com/broadinstitute/gatk/tree/master/scripts/cnv_wdl/germline One of the required parameters is: CNVGer...

    • Sheryl
    • 2 followers
    • 3 comments
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    Sheryl commented,

    1. Community
    2. General Discussion
    3. How to choose interval_list?

    Sorry - I meant using either: wgs_coverage_regions.hg38.interval_list or  wgs_evaluation_regions.hg38.interval_list

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    Sheryl commented,

    1. Community
    2. General Discussion
    3. How to choose interval_list?

    Thanks Laura Gauthier,   Could you just confirm for me which I should be using to get the median of the coverage over the autosome for the mitochondrial workflow? I assume it's just a case of using...

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    Sheryl commented,

    1. Community
    2. General Discussion
    3. How to choose interval_list?

    Hi Genevieve Brandt (she/her),   Do you have an answer for this please? I can't find documentation anywhere what the difference is between  the wgs_coverage_regions.hg38.interval_list and wgs_evalu...

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    Sheryl created a post,

    Mitochondrial pipeline requirement

    1. Community
    2. New User Advice

    I am wanting to use the GATK best practice for mitochondrial SNVs and indel variants. I read from here https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-di...

    • Sheryl
    • 4 followers
    • 4 comments
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    Sheryl created a post,

    ExomeSingleSample wdl

    1. Community
    2. New User Advice

    I'm trying to run the ExomeSingleSample wdl but for hg19 or GRCh37. I can't find any resources for this version e.g contam.exome_calling_regions.v1.UD, contam.exome_calling_regions.v1.bed,  contam....

    • Sheryl
    • 2 followers
    • 1 comment
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    Sheryl created a post,

    Best practice with read groups

    1. Community
    2. New User Advice

    Hi,  Could you clarify something for my own understanding please? I have read your post https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups  on read groups and understand wha...

    • Sheryl
    • 2 followers
    • 1 comment
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    Sheryl commented,

    1. Community
    2. Somatic
    3. strand bias and orientation bias

    Am I missing something? Are the first two figures not exactly the same??