nexus_calculate_cancer_cell_fraction

Calculate cancer cell fraction (CCF) for somatic DNA variants.

Usage

nexus_calculate_cancer_cell_fraction \
    --bam-file /path/to/file \
    --variants-tsv-file /path/to/file.tsv \
    --copy-number-tsv-file /path/to/file.tsv \
    --tumor-purity 0.5 \
    --sex female \
    [--normal-ploidy 2] \
    [--min-base-quality 0] \
    [--min-mapping-quality 0] \
    [--anchor-bp 20] \
    [--num-threads 4] \
    --output-tsv-file /path/to/file.tsv

Parameters

Parameter	Type	Default	Description
--bam-file	Path	required	Tumor BAM file.
--variants-tsv-file	Path	required	Somatic DNA variants TSV file. Expected columns: variant_id, chromosome_1, position_1, strand_1, operation_1, chromosome_2, position_2, strand_2, operation_2, sequence, position_1_read_count_alternate_allele, position_2_read_count_alternate_allele.
--copy-number-tsv-file	Path	required	Copy number TSV file. Expected columns: chromosome, start, end, copy_number, major_copy_number, minor_copy_number.
--tumor-purity	float	required	Tumor purity in (0, 1].
--sex	str	required	Sex. Sets the germline (normal-cell) copy number on the sex chromosomes (chrX: 1 (male) / 2 (female); chrY: 1 (male) / 0 (female)). This information is used for CN_normal in the CCF and multiplicity formulas and the off-segment fallback genotype. Autosomes use –normal-ploidy. Choices: male or female.
--normal-ploidy	int	2	Normal (germline) copy number on the autosomes (default: 2). Sex chromosomes are set by –sex, not this value.
--min-base-quality	int	0	Minimum base quality for pileup depth at substitution loci (default: 0).
--min-mapping-quality	int	0	Minimum mapping quality for reads counted in depth (default: 0).
--anchor-bp	int	20	Flanking matched bases required on each side of a breakpoint for a read to count as reference-spanning at junction variants (default: 20).
--num-threads	int	4	Number of htslib threads for BGZF decompression of the phased BAM (default: 4).
--output-tsv-file	Path	required	Output TSV file.