snippy-ng utils cnv

Estimate copy number variation from an aligned BAM or CRAM.

The command uses samtools coverage to calculate mean depth for each contig. By default, The largest contig is assumed to have one copy number. Other contigs are assigned rounded integer copy numbers from their depth relative to that baseline.

Contig Copy Number

Estimate copy number for each contig:

snippy-ng utils cnv sample.cram > sample.cnv.tsv

Output:

contig_id   read_depth  copy_number

Feature Copy Number

Supply a GFF to estimate copy number for each selected feature. The default feature type is gene.

snippy-ng utils cnv sample.cram --gff reference.gff > sample.features.cnv.tsv

Use another GFF feature type:

snippy-ng utils cnv sample.cram --gff reference.gff --feature gene > sample.genes.cnv.tsv

Feature mode uses samtools depth -aa -b and reports the median per-base depth for each feature.

Output:

feature_id  contig_id   start   end read_depth  copy_number

Known Single-Copy Baseline

Use a known single-copy interval on the largest contig as the baseline:

snippy-ng utils cnv sample.cram --known-single-copy 4518,5000 > sample.cnv.tsv

Use an explicit contig:

snippy-ng utils cnv sample.cram --known-single-copy chr1:4518-5000 > sample.cnv.tsv

The known single-copy interval can also be used with feature mode:

snippy-ng utils cnv sample.cram \
  --gff reference.gff \
  --known-single-copy 4518,5000 \
  > sample.features.cnv.tsv

The baseline is the median per-base depth across the known single-copy region.

Options

Option	Purpose
ALIGNMENT	Input BAM or CRAM.
--gff PATH	Estimate copy number per selected GFF feature instead of per contig.
--feature TEXT	GFF feature type to use with --gff; default gene.
--known-single-copy TEXT	Baseline interval as START,END on the largest contig or CONTIG:START-END.
--no-header	Do not print the TSV header.