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GATK Structural Variants Pipeline - Steps

Hi all!

I am writing this question to ask, where can I find the exact steps used in the GATK Structural Variants Pipeline?

I understand that there are various pipelines, my goal is to compare the GATK Somatic Short Variant pipeline (SNPs and short indels) to the GATK Somatic Structural Variants. Particularly, I am searching for a schematic that ilustrate each step of both pipelines from fasta to vcf/maf.

This blogpost https://gatk.broadinstitute.org/hc/en-us/articles/9022487952155-Structural-variant-SV-discovery mentions the steps in general I would like one with all steps.

Sorry if it is a too general question but I believe that having this question would facilitate researchers finding this resources.

Note: Structural variants (SVs) are DNA rearrangements that involve at least 50 nucleotides: The variants that this GATK-SV is able to detect:

  • Copy number variants (CNVs), including deletions and duplications
  • Insertions
  • Inversions
  • Reciprocal chromosomal translocations
  • Complex structural variants involving two or more distinct SV signatures in a single mutational event
sv gatk variant-calling
• 1,775 views • link
updated by Ram Ram • written by Bioinformatics_begginner • Bioinformatics_begginner

Thank you for the response, I mean those tools aren't all the steps from fasta to vcf. Would be key understanding the aligner, reference used, if they use mark duplicates, ... and compare the short variant / indel pipeline (best practices) that uses Mutect vs the GATK-SV that uses (Manta, MELT, and Wham for SV / cn.MOPS and GATK gCNV for copy-number variations)

• 0 views • link
written by Bioinformatics_begginner • Bioinformatics_begginner

1 answer

A structural variation pipeline for short-read sequencing

https://github.com/broadinstitute/gatk-sv

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written by Pierre Lindenbaum Pierre Lindenbaum

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