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meraj

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Username
meraj
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India
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  • @serhat_t said: Hi @Sheila, I have a problem with using CalculateGenotypePosteriors and VariantAnnotator tools. First, I run CalculateGenotypePosteriors on a VCF file of a jointly called trio (mother, father, child). I can see the relevant…
  • @bhanuGandham Hi, I changed the command as below and it works now: java -jar gatk-package-4.0.9.0-local.jar \ VariantRecalibrator \ -R path_to_hum_ref/hg38_file.fasta -V combined_GRC_mak1_hg38.finalvars.vcf \ -an QD -an MQ -an MQRankSum -an…
  • @Geraldine_VdAuwera Hi, I changed the filename prefix 1000G with thouzndG in the command (guessed cz syntax error), and now it works. Thanks. Best, Meraj
  • @ahmed_chakroun said: Hi, I have the exact same problem with both files used within theses options: --resource omni,known=false,training=true,truth=false,prior=12.0:1000G_omni2.5.hg38.vcf.gz --resource 1000G,known=false,training=tru…
  • Hi @skngs , Now the error reads as below: A USER ERROR has occurred: Argument resource has a bad value: 1000G,known=false,training=true,truth=false,prior=10.0:1000G_phase1.snps.high_confidence.hg38.vcf.gz. Problem constructing FeatureInput fro…
  • Hi, I am unable to run analysis for variant recalibration using GATK. I am posting the script as below: java -jar gatk-package-4.0.9.0-local.jar \ VariantRecalibrator \ -R path_to_hum_ref/hg38_file.fasta -V combined_GRC_mak1_hg38.finalvars.vc…