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Heba B abusamra

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Recent activity by Heba B abusamra Sort by recent activity Recent activity Votes

  • Error using FindBreakpointEvidenceSpark

    Answered
    1. Community
    2. Germline

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used:    v.4.2.2b) Exact command used: /app/Genome/gatk-4.2.2.0/gatk FindBreakpointEvidenceSpark \-I Data/GM24385_2_S15.bam \ ...

    • Heba B abusamra
    • 2 followers
    • 7 comments
    • 0 votes

  • StructuralVariationDiscoveryPipelineSpark vs GermlineCNVCaller

    1. Community
    2. General Discussion

    Dear  I need to understand the difference between StructuralVariationDiscoveryPipelineSpark tool and  GermlineCNVCaller As I knowledge the CNV is part of SV  "Structural variation (SV) is generally...

    • Heba B abusamra
    • 2 followers
    • 1 comment
    • 0 votes

  • DRAGEN-GATK short variant calling

    Answered
    1. Community
    2. General Discussion

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: latest version 4.2.2.0 No an error accures. However, I want to use the dragen-gatk model and Im using these command. Is ...

    • Heba B abusamra
    • 3 followers
    • 2 comments
    • 0 votes

  • Genotype 0/1 for variants with VAF=80%

    1. Community
    2. Germline

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: v4.1.8b) Exact command used: gatk HaplotypeCaller -R ../../genome/genome.fa -I Alignment_Germline_Aziz/$i.bam --dbsnp .....

    • Heba B abusamra
    • 2 followers
    • 1 comment
    • 0 votes

  • CheckFingerprint (Picard) error message

    Answered
    1. Community
    2. Germline

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used:  gatk-4.1.8.1 b) Exact command used: /app/Genome/gatk-4.1.8.1/gatk CheckFingerprint \--DETAIL_OUTPUT PBG-561-20R_S6-Fi...

    • Heba B abusamra
    • 3 followers
    • 5 comments
    • 0 votes

  • Haplotype database for finger print

    1. Community
    2. Germline

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: b) Exact command used: c) Entire error log: If not an error, choose a category for your question(REQUIRED):a)How do I (....

    • Heba B abusamra
    • 2 followers
    • 3 comments
    • 0 votes

  • Germline CNV vs HaplotypeCaller/indels

    1. Community
    2. Documentation Questions

    I have a question. What is the difference in the indels called from haplotypecaller and germline CNV. Is the deletion variant detected in  haplotypeCaller has to be present in the vcf generated fro...

    • Heba B abusamra
    • 2 followers
    • 1 comment
    • 0 votes

  • Germline CNV Results Interpretation

    Answered
    1. Community
    2. General Discussion

    (REQUIRED) Please provide: a) GATK version used: 4.1.8.1 I ran the whole gCNV pipeline for WES samples successfully, thanks to your guidelines. Now I have 2 outputs: 1.genotyped-segments-POCG-490-2...

    • Heba B abusamra
    • 4 followers
    • 3 comments
    • 0 votes

  • Germline CNV for WES data:FilterIntervals/ GermlineCNVCaller error

    1. Community
    2. Germline

    (REQUIRED) For us to most effectively understand your question, please fill in your responses below: a) I am using GATK version (v.4.1.8.1) b) The specific command(s) I used is/are gatk PreprocessI...

    • Heba B abusamra
    • 3 followers
    • 4 comments
    • 0 votes

  • Germline CNV Probabilities must be non-negative error

    1. Community
    2. Germline

    Can you please provide a) GATK version used : GATKv4.1.4b) Exact GATK commands used : DetermineGermlineContigPloidyc) The entire error log if applicable. Im following gCNV pipeiline on https://gatk...

    • Heba B abusamra
    • 5 followers
    • 8 comments
    • 0 votes