iarcbioinfo/facets-nf repository overview

⁠facets-nf

⁠Pipeline using facets for fraction and copy number estimate from tumor/normal sequencing

⁠UNDER DEVELOPMENT

⁠Description

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⁠Dependencies

1. 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.
2. External software:

• facets⁠

You can avoid installing all the external software by only installing Docker. See the IARC-nf⁠ repository for more information.

⁠Input (mandatory)

⁠Parameters

• ⁠Mandatory

Dbsnp vcf reference can be downloaded for:

• hg19: wget ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/VCF/00-common_all.vcf.gz

• hg38: wget ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/VCF/00-common_all.vcf.gz

  • ⁠Optional

• ⁠Flags

Flags are special parameters without value.

⁠Usage

nextflow run iarcbioinfo/facets-nf --tumor_bam_folder path/to/T_BAMS --normal_bam_folder path/to/N_BAMS --analysis_type genome --ref hg38 --dbsnp_vcf_ref path/to/dbSNP_vcf_ref.vcf.gz 

⁠Output

In Sample.RData:

• xx corresponds to the pre-processed data using the segmentation critical value cval_preproc (output of function preProcSample)

• oo_large corresponds to the processing of xx using the segmentation critical value cval_proc1 (output of function procSample(xx,cval = cval_proc1,...) )

• fit_large: cluster specific copy number and cellular fraction (output of emcncf(oo_large))

• oo_fine corresponds to the processing of xx using the segmentation critical value cval_proc2 (output of procSample(xx, cval = cval_proc2, ...))

• fit_fine: cluster specific copy number and cellular fraction ( output of emcncf(oo_fine))

⁠Common errors

In case of low coverage you may get the following error during facets process:

Loading required package: pctGCdata
Error in fit.cpt.tree(genomdat, cval = cval, hscl = hscl, delta = delta) :
NA/NaN/Inf in foreign function call (arg 9)
Calls: preProcSample -> segsnps -> fit.cpt.tree

=> We advise then to decrease the parameter: min_read_count

⁠Directed Acyclic Graph

⁠Contributions