/fair_cnv_facets

Snakemake workflow designed to call CNV using Facets

Primary LanguagePythonMIT LicenseMIT

Snakemake GitHub actions status

Do not use. Active dev.

Snakemake workflow used to call somatic CNV with Facets

Usage

The usage of this workflow is described in the Snakemake workflow catalog it is also available locally on a single page.

Results

A complete description of the results can be found here in workflow reports.

Material and Methods

The tools used in this pipeline are described here textually. Web-links are available below:

workflow_rulegraph

Index and genome sequences with fair_genome_indexer

Get DNA sequences

Step Commands
Download DNA Fasta from Ensembl ensembl-sequence
Remove non-canonical chromosomes pyfaidx
Index DNA sequence samtools
Creatse sequence Dictionary picard

Get genome annotation (GTF)

Step Commands
Download GTF annotation ensembl-annotation
Fix format errors Agat
Remove non-canonical chromosomes, based on above DNA Fasta Agat
Remove <NA> Transcript support levels Agat

Get dbSNP variants

Step Commands
Download dbSNP variants ensembl-variation
Filter non-canonical chromosomes pyfaidx + BCFTools
Index variants tabix

Bowtie2 Mapping with fair_bowtie2_mapping

Align reads over the genome

Step Meta-Wrapper Wrapper
Bowtie2-build bowtie2-sambamba meta-wrapper bowtie2-build
Fastp fastp
Bowtie2-align bowtie2-sambamba meta-wrapper bowtie2-align
Sambamba sort bowtie2-sambamba meta-wrapper sambamba-sort
Sambamba-view bowtie2-sambamba meta-wrapper sambamba-view
Sambamba-markdup bowtie2-sambamba meta-wrapper sambamba-markdup
Sambamba-index bowtie2-sambamba meta-wrapper sambamba-index

Quality controls

Step Wrapper
Picard picard-collectmultiplemetrics
Samtools samtools-stats
FastQC fastqc-wrapper
MultiQC multiqc-wrapper

Call CNV with Facets

Step Wrapper
Facets cnv_facets

Quality controls

Step Wrapper
MultiQC multiqc-wrapper