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

CreateSomaticPanelOfNormals (BETA) Follow

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     I tried to use this tutorial to generate a PON using The Genome Analysis Toolkit (GATK) v4.4.0.0. 

    when i runned the following command the temp directory was full of json files so the ejecution died,

    singularity run -H /mnt/bioinfnas2/bioinformatics/projects/panel_jordi:/home/ gatk4.sif gatk GenomicsDBImport -R ref/Homo_sapiens_assembly38.fasta -L ref/GRCh38.bed --genomicsdb-workspace-path pon_db -V vcf/PMP35_blood.recal.cram.vcf.gz -V vcf/BL_T243.recal.cram.vcf.gz -V vcf/PMP21_blood.recal.cram.vcf.gz -V vcf/PMP3_blood.recal.cram.vcf.gz -V vcf/PMP12_blood.recal.cram.vcf.gz -V vcf/PMP18_blood.recal.cram.vcf.gz -V vcf/PMP28_blood.recal.cram.vcf.gz -V vcf/BL_T225.recal.cram.vcf.gz -V vcf/PMP32_blood.recal.cram.vcf.gz -V vcf/PMP33_blood.recal.cram.vcf.gz -V vcf/BL_T251.recal.cram.vcf.gz -V vcf/BL_T233.recal.cram.vcf.gz -V vcf/PMP47_blood.recal.cram.vcf.gz -V vcf/PMP39_BLOOD.recal.cram.vcf.gz -V vcf/PMP46_blood.recal.cram.vcf.gz -V vcf/PMP15_blood.recal.cram.vcf.gz -V vcf/PMP17_blood.recal.cram.vcf.gz -V vcf/BL_T217.recal.cram.vcf.gz -V vcf/BL_T241.recal.cram.vcf.gz -V vcf/PMP29_blood.recal.cram.vcf.gz -V vcf/BL_T262.recal.cram.vcf.gz -V vcf/BL_T247.recal.cram.vcf.gz -V vcf/PMP1_blood.recal.cram.vcf.gz -V vcf/PMP24_blood.recal.cram.vcf.gz -V vcf/PMP41_blood.recal.cram.vcf.gz -V vcf/PMP42_blood.recal.cram.vcf.gz -V vcf/PMP43_blood.recal.cram.vcf.gz -V vcf/BL_T244.recal.cram.vcf.gz -V vcf/BL_T265.recal.cram.vcf.gz

    how could I solve this problem?




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