VARIANT-CALLING-AMPLISEQ (✓ PRODUCTION)

Version: 1.0.0 Tags: AmpliSeq / Variant Calling / Flamingo / Automated

This is the fully automated pipeline for Ampliseq on Flamingo. No config, no design, no time wasted.

« A good pipeline has no documentation » Someone at BiGR

Pipeline dependencies

This pipeline requires the following packages to be run. Any other additional requirements are being installed dynamically.

Conda:

  • conda-forge::python ==3.9.2

  • conda-forge::git ==2.30.2

  • conda-forge::jinja2 ==2.11.3

  • conda-forge::pygraphviz ==1.7

  • conda-forge::flask ==1.1.2

  • conda-forge::pandas ==1.2.3

  • conda-forge::zlib ==1.2.11

  • conda-forge::openssl ==1.1.1k

  • conda-forge::networkx ==2.5.1

  • bioconda::snakemake ==6.1.1

  • conda-forge::black ==20.8b1

  • conda-forge::singularity ==3.7.1

  • conda-forge::mamba ==0.9.2

Additionally, the following prerequisites are non-optional:

  • None. Everything is on Flamingo already.

Input files

Please find below the list of required input files:

  • Several paried fastq files.

Output files

Please find below the list of expected output files:

  • Annotated VCF files

  • MultiQC report

Notes

This pipeline takes the cold storage into account. No need to copy your data in advance.

No maftools compatibility at this point.

List of tools: rsync/ln -> Fastp -> BWA -> Samtools/GATK/Picard -> Mutect2/Vascan2 -> Snpsift/SnpEff -> MultiQC

Bam files are corrected before Varscan2 with GATK pipeline. Raw bam are passed to Mutect2 since GATK advises to do so.

Mutect2 calling are filtered following best practices. Varscan2 calling are filtered on padj <= 0.05.

Installation

While installing the workflow, you may run the following commands (order matters):

Case

Command line

none

 
# No installation needed.

Testing

In order to test the pipeline, you may try the following commands:

Case

Command line

quick-test

 
bash /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/variant_calling_ampliseq/test.sh

verbose-test

 
bash -x /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/variant_calling_ampliseq/test.sh

Preparation

In order to prepare a run, you may try the following commands:

Case

Command line

none

 
# No preparation, everything is available.

Execution

In order to execute the pipeline, you may run the following commands:

Case

Command line(s)

hg19

 
bash /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/variant_calling_ampliseq/run.sh hg19

hg38

 
bash /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/variant_calling_ampliseq/run.sh hg38