snippy-ng utils aln 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 aln 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. By default, the first feature type in the GFF is used.

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

Use another GFF feature type:

snippy-ng utils aln 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. Parsed GFF attributes are appended as additional columns. Missing attributes are reported as empty fields.

Output:

feature_id  contig_id   start   end read_depth  copy_number ID  biotype Name

Known Single-Copy Baseline

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

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

Use an explicit contig:

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

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

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

Use a known single-copy feature from the GFF as the baseline:

snippy-ng utils aln cnv sample.cram \
  --gff reference.gff \
  --known-single-copy-feature gene:WILD_00001 \
  > sample.features.cnv.tsv

The baseline is the median per-base depth across the known single-copy region or feature. Feature matching uses the reported feature ID or any exact GFF attribute value, such as ID, Name, gene, or locus_tag.

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; defaults to the first feature type in the GFF.
--known-single-copy-region TEXT	Baseline interval as START,END on the largest contig or CONTIG:START-END.
--known-single-copy-feature TEXT	Baseline feature ID or GFF attribute value from --gff.
--no-header	Do not print the TSV header.