Coordinate Corruption in Symbolic Alleles #225
Description
Splitting off symbolic alleles issue reported in #222 by @lbombini.
Original report:
When the VCF contains symbolic alleles, the pipeline produces an invalid (unsorted) VCF, preventing indexing.
Error Message:
[E :: hts_idx_push] Unsorted positions on sequence #1: 97173990 followed by 1
index: failed to create index for "/out/union_sorted.normalized.vcf.bgz"
Root Cause Analysis:
The normalization step handles symbolic alleles (specifically <DEL>) incorrectly. A variant at a valid genomic position is rewritten to position 1 with a reference allele of N.
- Pre-Normalization:
chr1:97175176 T > <DEL> - Post-Normalization:
chr1:1 N > <DEL>
This suggests the normalization logic is attempting to anchor or left-align a symbolic allele that lacks an explicit sequence, defaulting it to the start of the contig.