nucleus.examples.validate_vcf -- Validates that a VCF file and a FASTA reference file correspond.
Source code: nucleus/examples/validate_vcf.py
Documentation index: doc_index.md
They correspond if: a) they cover the same contigs, b) the reference covers every variant in the vcf file, and c) they agree on the reference bases covered by the variants.
Functions overview
| Name | Description |
|---|---|
main(argv) |
|
validate_contigs(ref_contigs, vcf_contigs) |
Validate that the two lists of ContigInfos have the same set of names. |
validate_variant(ref_reader, variant) |
Validate that variant is covered by the reference and agrees with it. |
Functions
main(argv)
validate_contigs(ref_contigs, vcf_contigs)
Validate that the two lists of ContigInfos have the same set of names.
validate_variant(ref_reader, variant)
Validate that variant is covered by the reference and agrees with it.