Description

Copy-number aberration calling with SAVANA for long-read tumour/normal alignments.

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

3 ()

4 ()

5 ()

6 ()

7 ()

0 ()

1 ()

2 ()

contigs (file)

Optional contigs list file for SAVANA to restrict analysis to specific contigs

*.txt

blacklist (file)

Optional blacklist BED for CNA analysis

*.bed

g1000_vcf (string)

Optional 1000G preset for allele counting (mutually exclusive with snp_vcf and allele_counts_het_snps)

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

Tools

savana Documentation

SAVANA: somatic SV and copy-number aberration caller for long-read data.

https://github.com/cortes-ciriano-lab/savanadoi: 10.1038/s41592-025-02708-0License: Apache-2.0
Authors