Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

GermlineCNVCaller/denoising_config.json

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    Bhanu Gandham

    Hi,

     

    Have you run in cohort mode to create the PON? PON is needed for case mode. The doc you shared above has more information on this.

     

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    Heba B abusamra

    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-merging-rule OVERLAPPING_ONLY -I PBG-1095-19_S2.tsv -I PBG-1077-19R_S8.tsv -I PBG-1076-19R_S7.tsv -I PBG-1096-19_S1.tsv --contig-ploidy-priors contig_ploidy_priors.tsv --output . --output-prefix ploidy --verbosity DEBUG

    /app/Genome/GATK-4.1.8.1/gatk DetermineGermlineContigPloidy --model ploidy-model -I POCG-490-20_S2.tsv -O . --output-prefix ploidy-case --verbosity DEBUG

    /app/Genome/GATK-4.1.8.1/gatk GermlineCNVCaller --run-mode CASE -I POCG-490-20_S2.tsv --contig-ploidy-calls ploidy-case-calls --model ploidy-model --output POCG-490-20 --output-prefix POCG-490-20 --verbosity DEBUG

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    Genevieve Brandt

    Please see this document under 3. Call autosomal and allosomal contig ploidy with DetermineGermlineContigPloidy https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants

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