milkschen / matchall

Accurate matching of variant alleles using local haplotypes

Matchall

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.

Installation

Dependencies - required

• Python (3.6+)
• pysam (0.15.3)

Dependencies. - optional (used in our data processing pipelines)

• bcftools (1.12)
• tabix (1.12)

Usage

Download

https://github.com/milkschen/matchall.git

Annotate

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

• Detailed tutorial for matchall-annotate

Compare

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

• Detailed tutorial for matchall-compare

Test

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

matchall's Issues

Supporting querying multiple database VCF

Currently a unified database VCF is required. But for some reference panels VCFs are provided chromosome-by-chromosome. Concatenating them is an additional cost, so it'll be nice to allow multiple db VCFs (either a file containing paths, or multiple arguments, or both).

Supporting user-defined tags

Currently only AF is supported. It'll be nice to support other tags. Remember to check if the database VCF contains the tag when implementing.