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Laura Sanz

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  • VariantRecalibrator error

    Hello, I have a multi-vcf file (10 WGS human samples, chr1) generated using HaplotypeCaller in GVCF mode, followed by GenomicsDBImport and GenotypeGVCFs. I am trying to use VariantRecalibrator but ...

  • VariantRecalibrator - Exception thrown at

    Hello, I have a multi-vcf file (10 WGS human samples, chr1) generated using HaplotypeCaller in GVCF mode, followed by GenomicsDBImport and GenotypeGVCFs. I am trying to use VariantRecalibrator but ...

  • Unable to trim uncertain bases without flow order information

    Answered

    Hi all, I am using GATK to call my variants (WGS) and am getting the error "Unable to trim uncertain bases without flow order information" when I run HaplotypeCaller. I added the read groups and va...

  • Found invalid line in index file - GATK

    Hi, I am using gatk-4.3.0.0 to call my variants. I download the .fasta .dict and .fasta.fai at https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0;tab=obje...