A bioinformatic workflow to call copy number variants reconstruct cell phylogenies from single-cell or spatial transcriptomics data
This is a workflow in nextflow to preprocess and use the numbat software for the analysis of single-cell or spatial transcromics data to study Copy number variations (CNVs).
- This pipeline is based on nextflow. As we have several nextflow pipelines, we have centralized the common information in the IARC-nf repository. Please read it carefully as it contains essential information for the installation, basic usage and configuration of nextflow and our pipelines.
- External software:
You can avoid installing all the external software by only installing Docker, and downloading the numbat docker file. See the IARC-nf repository for more information.
| Type | Description |
|---|---|
| input_file | Tab-separated file with columns ID (sample ID), matrix_folder (cellranger output folder with expression matrix .mtx, barcode, and features files), and bam (alignment files) |
| Name | Example value | Description |
|---|---|---|
| --gmap | /Eagle_v2.4.1/tables/genetic_map_hg38_withX.txt.gz | Path to genetic map provided by Eagle2 |
| --eagle | eagle | Path to Eagle2 binary file |
| --snpvcf | /data/genome1K.phase3.SNP_AF5e2.chr1toX.hg38.vcf | SNP VCF for pileup (e.g. genome1K.phase3.SNP_AF5e2.chr1toX.hg38.vcf) |
| --paneldir | /data/1000G_hg38 | Directory to phasing reference panel (e.g. 1000G_hg38) |
All these files can be downloaded from the numbat website, or are contained in the numbat docker container (note: the default paths correspond to the location within the docker container).
| Name | Default value | Description |
|---|---|---|
| --ncores | 8 | Number of cores to use. |
| --mem | 10 | Memmory (in Gb) to use. |
nextflow run script_nf.nf --input_file input.tsv [--OPTIONS] OPTION
| Name | Description | |
|---|---|---|
| Nicolas Alcala* | [email protected] | Developer to contact for support |
| Yanis Sindt-Baret | Developer | |
| Quentin Ohayon | Developer | |
| Natacha Doutrelea | Developer | |
| Claire Berthaud | Developer |
To work, the bam file needs to come with its index file (.bai); if necessary, it can be generated using the command:
samtools index -b BAME_FILE.bam