Heba B abusamra
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Recent activity by Heba B abusamra Sort by recent activity-
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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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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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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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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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 ...
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I have the same error can you explain how to create PON in cohort mode my commands /app/Genome/GATK-4.1.8.1/gatk DetermineGermlineContigPloidy -L target.preprocessed.interval_list --interval-mergi...