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Pipeline Index

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
edited July 2019 in Best Practices Workflows

This document is under construction. It aims to provide an overview of use cases covered by GATK Best Practices workflows.

Variant Discovery Germline Somatic Notes
Data pre-processing Single-sample Single-sample Same workflow applies to all
Short variants: SNPs and Indels Single-sample & Joint Calling Tumor-Normal & Tumor-Only
Copy Number Variants (CNVs) Multisample Tumor-Normal & Tumor-Only
Structural Variants (SVs) In progress TBD
Special use cases Notes
Metagenomic analysis (PathSeq)
Mitochondrial short variants
Liquid blood biopsy
Post edited by Geraldine_VdAuwera on


  • AzizAziz USAMember
    Hi Geraldine,
    I have used GATK for SNPcalling since 2016. I think when the last version released the old version did not work. I test both version but I got the same error.

    The error copied below:

    /var/spool/torque/mom_priv/jobs/4716059.brown-adm.rcac.purdue.edu.SC: line 24: GenomeAnalysisTK: command not found

    my pipeline is:
    GenomeAnalysisTK -nt 23 -T RealignerTargetCreator -R branch_gene.fasta -I JHIN01_WG_aligned_dedup.bam -o forIndelRealigner_JHIN01.intervals
    GenomeAnalysisTK -T IndelRealigner -R branch_gene.fasta -I JHIN01_WG_aligned_dedup.bam -targetIntervals forIndelRealigner_JHIN01.intervals -o sorted_JHIN01_WG_aligned.bam
    GenomeAnalysisTK -T HaplotypeCaller -R branch_gene.fasta -I sorted_JHIN01_WG_aligned.bam --emitRefConfidence GVCF -variant_index_type LINEAR -variant_index_parameter 128000 -nct 23 -o variants_JHIN01_WG.g.vcf
  • AzizAziz USAMember
    I highly appreciate your help.
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