Do not use. Active dev.
Snakemake workflow used to call somatic CNV with Facets
The usage of this workflow is described in the Snakemake workflow catalog it is also available locally on a single page.
A complete description of the results can be found here in workflow reports.
The tools used in this pipeline are described here textually. Web-links are available below:
Index and genome sequences with fair_genome_indexer
Step | Commands |
---|---|
Download DNA Fasta from Ensembl | ensembl-sequence |
Remove non-canonical chromosomes | pyfaidx |
Index DNA sequence | samtools |
Creatse sequence Dictionary | picard |
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 |
Step | Commands |
---|---|
Download dbSNP variants | ensembl-variation |
Filter non-canonical chromosomes | pyfaidx + BCFTools |
Index variants | tabix |
Bowtie2 Mapping with fair_bowtie2_mapping
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 |
Step | Wrapper |
---|---|
Picard | picard-collectmultiplemetrics |
Samtools | samtools-stats |
FastQC | fastqc-wrapper |
MultiQC | multiqc-wrapper |
Step | Wrapper |
---|---|
Facets | cnv_facets |
Step | Wrapper |
---|---|
MultiQC | multiqc-wrapper |