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stella

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Latest activity by stella
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    stella commented,

    Hi Genevieve Brandt (she/her) Thanks for your helpful answer. :)  Oh

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    stella commented,

    Hi Genevieve Brandt (she/her) Thanks for your response. I'll just make three more clear.   Q1. Is this the way you said it? 1) Run 200 in cohort mode to get model and VCF files 2) (Of 300 samples...

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    stella created a post,

    Error in document

    Answered

    Dear GATK team,  Hi I'm Oh.  There seems to be a problem with the tutorial. https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants...

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    stella created a post,

    [Genotype Refinement] Abnormal results.

    I did Genotype refinement process as belows.  $GATK4_CMD --java-options "-Xms8g -Xmx8g" \ CalculateGenotypePosteriors \ -supporting 1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf \ -V ...

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    stella commented,

    Thanks for your reply. :) Then, I can't find the meaning of genotype ( "./.").  Thanks.   Oh. 

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    stella created a post,

    [HaplotypeCaller] I can't understand this results.

    Answered

    Hi,  I executed HaplotypeCaller and GenomicDBimport (GATK version 4.1.4.1).    First Question. In my haplotypeCaller results (sample names = 2016000051),  there is no variant on chr1:10363 as below...

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    stella commented,

    Dear Bhanu Gandham,    Thanks for your reply.   Sincerely yours,   Stella.

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    stella created a post,

    About haplotypecaller (for large samples)

    Answered

    Dear GATK team,  Hi I'm Stella.  I have a question.  I have 400 BAMs comprised of 200 healthy people BAMs, and 200 Cancer patients BAMs. For 400 BAMs, I ran HaplotypeCaller on each BAMs. My Questio...

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    stella commented,

    Hi Jason,  I appreciate your reply.  Sincerely yours, Stella  

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    stella created a post,

    XS tag in SAM file

    Dear GATK team, Hi. I'm oh. I have questions about pre-processed bam by GATK4 pipeline (https://github.com/gatk-workflows/gatk4-data-processing/blob/master/processing-for-variant-discovery-gatk4.wd...