Avatar

Laura Sanz

Follow
  • Total activity 13
  • Last activity
  • Member since
  • Following 0 users
  • Followed by 0 users
  • Votes 1
  • Subscriptions 5

Activity overview

Latest activity by Laura Sanz
  • Avatar

    Laura Sanz commented,

    1. Tool Index
    2. 4.0.1.2
    3. IndexFeatureFile

    Please update for GATK 4.3 "A USER ERROR has occurred: feature-file is not a recognized option"

  • Avatar

    Laura Sanz created a post,

    VariantRecalibrator error

    1. Community
    2. Germline

    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 ...

    • Laura Sanz
    • Edited
    • 2 followers
    • 1 comment
    • 0 votes
  • Avatar

    Laura Sanz commented,

    1. Community
    2. Germline
    3. VariantRecalibrator - Exception thrown at

    Thanks for your comment SkyWarrior I have read-write access in the output directory. I also tried moving --tmp-dir to another directory and it didn't work. 

  • Avatar

    Laura Sanz created a post,

    VariantRecalibrator - Exception thrown at

    1. Community
    2. Germline

    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 ...

    • Laura Sanz
    • Edited
    • 2 followers
    • 3 comments
    • 0 votes
  • Avatar

    Laura Sanz commented,

    1. Community
    2. Germline
    3. Unable to trim uncertain bases without flow order information

    Hi Allison, Those bam files had been generated using minimap2. I repeated the mapping to reference with bwa (https://github.com/lh3/bwa) and the problem got solved.  I hope it helps. Laura  

  • Avatar

    Laura Sanz created a post,

    Unable to trim uncertain bases without flow order information

    Answered
    1. Community
    2. Germline

    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...

    • Laura Sanz
    • Edited
    • 5 followers
    • 8 comments
    • 0 votes
  • Avatar

    Laura Sanz created a post,

    Found invalid line in index file - GATK

    1. Community
    2. General Discussion

    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...

    • Laura Sanz
    • 1 follower
    • 0 comments
    • 0 votes