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stella

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Latest activity by stella
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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.

    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)

    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...

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    stella created a post,

    Haplotypecaller usage (version decrepancy)

    Hi all,  I have a question.  First of all, I have 400 DNA (from extracted blood cells) derived bam files.  And I want to detect germline variants using consolidate and joint genotyping.  Then, coul...