CNV2VCF

CNV2VCF is a tool to convert output of ClinCNV to VCF format.

DEL/DUP interpretation is not (yet) gender aware for the X chromosome.

Custom info fields

The following custom INFO fields are added to the VCF:

NOREGIONS: Number of regions in the CNV (no_of_regions)
PAF: Potential allelic fraction (potential_AF)
GENES: List of genes affected by the CNV (genes)
QVALUE: Q-value of the CNV (qvalue)
OLAPAFIMGAG: Overlap with inhouse database of IMGAG and GnomAD (overlap af_genomes_imgag)
CNPATO: Known pathogenic CNVs (cn_pathogenic)
CLINVAR: ClinVar overlapping CNVs (clinvar_cnvs)
GENEINFO: Gene informations (i.e. stringency, region, etc.) (gene_info)
IHPATO: Known CNVs in inhouse database (ngsd_pathogenic_cnvs)

-r REFERENCE, --reference REFERENCE reference genome in FASTA format.
-i INPUT [INPUT ...], --input INPUT [INPUT ...] input file(s) in ClinCNV TSV format.
-s SAMPLEID [SAMPLEID ...], --sampleid SAMPLEID [SAMPLEID ...] sample id(s). Will be infered from input filename if not given.
-c CONFIDENCEINTERVAL, --confidenceinterval CONFIDENCEINTERVAL confidence interval around POS/END for imprecise variants. Will be used in in both directions. Defaults to 500 resulting in CIPOS=-500,500;CIEND=-500,500.

Uses pyfaidx (see Shirley MD, Ma Z, Pedersen BS, Wheelan SJ. 2015. Efficient "pythonic" access to FASTA files using pyfaidx. PeerJ PrePrints 3:e970v1 https://doi.org/10.7287/peerj.preprints.970v1)