clincnv_overlapper

ClinCNV-Overlapper

Helps to calculate overlaps between samples. Works in two modes:

• normal-only would calculate overlaps within supplied samples list
• normal and tumors mode would calculate overlaps within each group of samples, and then it would get tumor results and filter any regions from normal one.

Installation

go install github.com/overerd/clincnv_overlapper@latest

Arguments

Required:

• -n|--normals or -t|--tumors expect a file with tab-separated values like {SAMPLE} normal/{SAMPLE}/{SAMPLE}_cnvs.tsv and SAMPLE somatic/{TUMOR}-{NORMAL}/CNAs_{TUMOR}-{NORMAL}.txt for germline and somatic ClinCNV results respectively for each sample, where {SAMPLE}, {TUMOR} and {NORMAL} are sample codes from coverage matrix.
• -o|--output sets path for output file.

Optional:

• -m|--min-overlap sets filter for minimum overlap power to select final regions (default: 2).
• --max-qvalue provides filtration with maximum QValue (default: 1.0).
• -b|--bed your_panel.bed provides bed file for regions gene annotation.
• --bed-gene-index shows program what column is to be used from bed file for regions gene annotation (default: 4).
• --buffer-size sets buffer size in bytes for reading ClinCNV files (should be set and increased if necessary to avoid "take too long" error when reading ClinCNV files with long lines) (default: 100 * 1024).
• -x|--genes-exclude-filter provides multiline file with exclude patterns for gene names.
• -f|--output-field-separator provides a string for separation fields in genes and samples columns (default: " | ").
• -s|--output-separator provides a string for columns separation (default: "\t").

Example

clincnv_overlapper \
    --normals data/normals_list.txt \
    [--tumors data/tumors_list.txt] \
    [--bed your_panel.bed] \
    [--bed-gene-index 5] \
    [--genes-exclude-filter data/gene_filters.txt] \
    --min-overlap 2 \
    [--buffer-size 1048576] \
    --max-qvalue 0.05 \
    --output-field-separator "; " \
    --output-separator "\t" \
    --output data/clincnv_overlaps.tsv

TODO

Dependency akamensky/argparse would be soon replaced.