stella
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Activity overview
Latest activity by stella-
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...