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Linda Do

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  • Error remove 0x1 from alternate contigs tutorial

    Answered

    Hi! Hi! I am trying to follow this tutorial: https://gatk.broadinstitute.org/hc/en-us/articles/360037498992--How-to-Map-reads-to-a-reference-with-alternate-contigs-like-GRCH38 and am stuck at the s...

  • Error HaplotypeCaller from alternate contigs tutorial

    Answered

    Hi! I am trying to follow this tutorial: https://gatk.broadinstitute.org/hc/en-us/articles/360037498992--How-to-Map-reads-to-a-reference-with-alternate-contigs-like-GRCH38 and I got the error below...

  • Alt Contig tutorial question

    Answered

    Hi! I am currently looking at the GATK tutorial for "(How to) Map reads to a reference with alternate contigs like GRCH38" (https://gatk.broadinstitute.org/hc/en-us/articles/360037498992--How-to-Ma...

  • Map reads with alternate contigs

    Answered

    Hi, I am new to GATK. In the tutorial for (How to) Map reads to a reference with alternate contigs like GRCH38 (https://gatk.broadinstitute.org/hc/en-us/articles/360037498992--How-to-Map-reads-to-a...

  • Reference Fasta vs Alt Reference Fasta

    Hi! Questions category: What does (......) mean? I'm new to GATK and I was trying to follow this tutorial: https://gatk.broadinstitute.org/hc/en-us/articles/360037498992--How-to-Map-reads-to-a-refe...

  • Error: GATK Terra HaplotypeCaller Workflow

    Hello! If you are seeing an error, please provide(REQUIRED) : a) GATK version used: Terra I am trying to use https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-di...

  • Resource bundle error download

    Hello! I am currently trying to download Homo_sapiens_assembly38.dbsnp138.vcf from the resource bundle from https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg3...

  • What is cohort?

    Answered

    Hello! I am new to GATK and am wondering which Best Practices Workflows in this page https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- is ...

  • Genotype Refinement Workflow wrong output

    Hello! I'm new to GATK and Unix. I have been following the Genotype Refinement Workflow for Germline Short Variants https://gatk.broadinstitute.org/hc/en-us/articles/360035531432-Genotype-Refinemen...

  • Warning: Reading will be unbuffered.

    Answered

    Hello! I am trying to use liftover a vcf file from hg19 to hg38. I don't get any error messages but I do get warning messages that confuse me. a) GATK version used: gatk-4.1.8.0b) Exact GATK comman...