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Heba B abusamra

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Latest activity by Heba B abusamra
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    Heba B abusamra commented,

    It gave me an error when using  --java-options -Xmx with gatk. However I used it with gatk-package-4.2.2.0-local.jar. Unfortunately I still get the same problem  java -Xms200m -jar /app/Genome/gatk...

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    Heba B abusamra commented,

    Here it is /app/Genome/gatk-4.2.2.0/gatk FindBreakpointEvidenceSpark \-I Data/GM24385_2_S15.bam \--aligner-index-image reference.fasta.img \--kmers-to-ignore kmers_to_ignore.txt \--spark-runner LOC...

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    Heba B abusamra commented,

    Thank you for your reply  I'm using HPC ~200G memory , and tried what you recommends regarding specifying executor cores to use but still have same problem 

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    Heba B abusamra created a post,

    Error using FindBreakpointEvidenceSpark

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    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 \ ...

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    Heba B abusamra created a post,

    StructuralVariationDiscoveryPipelineSpark vs GermlineCNVCaller

    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...

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    Heba B abusamra created a post,

    DRAGEN-GATK short variant calling

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    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 ...

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    Heba B abusamra created a post,

    Genotype 0/1 for variants with VAF=80%

    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 .....

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    Heba B abusamra commented,

    Thank you for your reply  what do you mean  by "your index" is it  the PBG-561-20R_S6.bam.bai  or reference dictionary file? actually the same sample was  aligned and used with haplotypeCaller with...

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    Heba B abusamra created a post,

    CheckFingerprint (Picard) error message

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    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...

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    Heba B abusamra commented,

    Thanks for your help I already read the link, however the link https://software.broadinstitute.org/gatk/documentation/article?id=9526  is not working --HAPLOTYPE_MAP -H   The file lists a set ...