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Recent activity by stella Sort by recent activity Recent activity Votes
  • [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 ...

  • [HaplotypeCaller] I can't understand this results.

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

  • 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...

  • 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...

  • 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...