Heba B abusamra
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Activity overview
Latest activity by Heba B abusamra-
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
AnsweredIf 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
AnsweredIf 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
AnsweredIf 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 ...