matchall (MATCH ALLele) annotates a VCF with the information in another VCF.
The core allele matching algorithm is described in this preprint.
Example use case:
- filling the population allele frequency (
AF) field in a variant set using information in a reference panel. - comparing two VCFs to find shared and private variants
A variant can be represented in multiple formats. An example in the table below shows a variant in two forms. The ambiguity in variant representation can confound annotating and result in errors.
| POS | REF | ALT |
|---|---|---|
| 1 | GAC | GA |
| 2 | AC | A |
The matchall algorithm solves this issue by comparing a variant and a set of queried variants from another VCF using re-constructed local haplotypes.
This algorithm annotates variants accurately regardless of representation.
- Python (3.6+)
- pysam (0.15.3)
- bcftools (1.12)
- tabix (1.12)
https://github.com/milkschen/matchall.git
Annotate an INFO field in the VCF using such information from another VCF.
python src/annotate.py -v target.vcf.gz -q query.vcf.gz -r ref.fa -o out.vcf.gz
Compare two VCFs and optionally report intersected and private variants.
python src/compare.py -v A.vcf.gz -q B.vcf.gz -op A_0-B_1 -m annotate,private,isec -o A_0-B_1.vcf.gz -r ref.fa
Run both unit and end-to-end tests:
sh test_all.sh
Or run them separately:
python src/test_matchall.py
python src/test_end_to_end.py