GATK-gCNV-discovery-bash-pipeline (for exomes)

• This repository contains bash developed pipelines: gatk_cohort.sh,the GATK cohort training model, and gatk_case.sh, the pipeline for germline CNV discovery in case samples.
• These scripts have been developed at the Institute of Biological Chemistry of the School of Exact and Natural Science (IQUIBICEN), University of Buenos Aires.

gatk_cohort.sh

Generates the Cohort model for exome germline GATK-CNV discovery,according to gGATK-CNVs guidelines.

• Requirements:
• Tools:
  • GATK 4.1.0.0
  • gCNV computational python module gcnvkernel installed with user-conda(for details,look at: https://gatk.broadinstitute.org/hc/en-us/articles/360035889851) *Input:
  • the Reference genome used to generate sample BAMs
  • the Exome capture kit used for library preparation
  • COHORT sample BAMs
• Output:
  • A COHORT model to be used for CASE CNVs discovery
  • VCFs of CNVs calls for the COHORT samples.

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gatk_case.sh

Identify CNVs in case samples using the cohort model generated by gatk_cohort.sh.These cases should be samples sequenced under the same conditions of the cohort.

• Requirements:
• Tools:
  • GATK 4.1.0.0
  • gCNV computational python module gcnvkernel installed with user-conda(for details,look at https://gatk.broadinstitute.org/hc/en-us/articles/360035889851)
• Input:
  • Reference genome used to generate sample BAMs
  • ref.hg38.interval_list, generated in the COHORT mode, by gatk_cohort.sh
  • CASE sample BAMs
  • COHORT model
• Output:
  • VCF of CNV calls for CASE samples.

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