No result for output.transhes using VariantRecalibrator

Post author
Bello Folaniyi

Using the below script, the VariantRecalibrator process stopped without ant error message

#!/bin/bash
gatk --java-options "-Xmx30g -Xms30g" VariantFiltration \
   -R BROILER/referenceExcludeUnknownContigs.fasta \
   -V testrun/OUTPUT.vcf.gz \
   -O testrun/OUTPUT.Filteration.vcf.gz \
   --filter-name "MappingQuality30" --filter-expression "MQ0 > 30" 
   --filter-name "QualityDepth2" --filter-expression "QD < 2.0" \
   --filter-name "StrandBias60" --filter-expression "FS > 60.0" 
gatk VariantRecalibrator \
   -R BROILER/referenceExcludeUnknownContigs.fasta \
   -V testrun/OUTPUT.Filteration.vcf.gz \
   -AS \
   --resource:GRCg6a_dbsnp,known=true,training=false,truth=false,prior=2.0 gallus_gallus.vcf.gz \
   --resource:GRCg6a_validated_snp,known=false,training=true,truth=true,prior=12 correctedAll.vcf.gz \
   -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR \
   -mode SNP \
   -O testrun/output.AS.recal \
   --tranches-file testrun/output.AS.tranches \
   --rscript-file output.plots.AS.R
gatk ApplyVQSR \
   -R BROILER/referenceExcludeUnknownContigs.fasta \
   -V testrun/OUTPUT.Filteration.vcf.gz \
   -O testrun/OutputVQSR.vcf.gz \
   -AS \
   --ts_filter_level 99.0 \
   --tranches-file testrun/output.AS.tranches \
   --recal-file testrun/output.AS.recal \
   -mode SNP
ex

Comments

1 comment

  • Comment author
    Samantha (she/her)

    Hi Bello,
     
    Thanks for reaching out to Terra Support. Unfortunately, questions regarding GATK run on local computers is out of scope for Terra Support as we can only assist with issues that relate to the Terra platform.
     
    Your question may be better suited for the GATK forum: https://gatk.broadinstitute.org/hc/en-us/community/topics. I would suggest reviewing recent posts to see if your question has already been answered, and if not you can create a new post.
     
    Best,
    Samantha

     
    0

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