collapse-bubble

(under development)

SV merging for pangenome VCF generated by minigraph-cactus pipeline and decomposed by vcfwave. It uses Truvari's API to merge similar SVs within the same bubble, e.g., highly polymorphic INS at the same position.

Overview

Input:

• multiallelic graph VCF generated by minigraph-cactus pipeline and processed by vcfbub

Preprocess:

• split into biallelic: bcftools norm -m -any
• annotate VCF and assign unique variant ID: scripts/annotate_var_id.py
• decompose VCF: vcfwave
• annotate, normalize and sort VCF: bcftools +fill-tags wave.vcf.gz -- -t AC,AN,AF | bcftools norm -f ref.fa | bcftools sort

SV merging (scripts/collapse_bubble.py)

1. Merged VCF (unsorted):

• INFO/ID_LIST: list of collapsed SVs
• INFO/TYPE: type of variant (SNP, MNP, INS, DEL, INV, COMPLEX)
• INFO/REFLEN: len(ref)
• INFO/SVLEN: len(alt) - len(ref)
• FORMAT/GT: merged genotypes

2. SV merging results in tsv format, e.g.:

CHROM   POS      Bubble_ID   Variant_ID             Collapse_ID
chr1    10039    >123>456    >123>456.COMPLEX.1_1   >123>456.COMPLEX.1_1
chr1    10040    >123>456    >123>456.COMPLEX.1_2   >123>456.COMPLEX.1_1

Postprocess:

• sort VCF: bcftools sort merged.vcf.gz
• merge duplicated variants: scripts/merge_duplicates.py

Dependency

truvari
pysam
pandas
numpy