Haplotypecaller

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Mahdi Ahmadi

• May 30, 2022 16:45

REQUIRED for all errors and issues:
a) GATK version used: gatk-4.2.6.0
b) Exact command used: gatk-4.2.6.0/gatk --java-options -Xmx4G HaplotypeCaller -R hg19.fa -I bqsr_dup_HG00121.chrom20_1.bam -O bqsr_hg00121_chrom20.g.vcf -bamout H_bqsr_dup_HG00121.chrom20_1.bam -ERC GVCF

c) Entire program log:I am running upper code but my output GVCF and bamout are empty

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  Genevieve Brandt (she/her)

  • May 31, 2022 17:16

  Hi Mahdi Ahmadi,

  Your post is missing the complete program log output from HaplotypeCaller. Please provide this information so that we can help troubleshoot.

  Best,

  Genevieve

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