I'm using Gingr (v1.3) to visualize SNPs and I found that certain VCF files are displayed incorrectly. This happens when the ref or alt columns in the VCF files are lowercase instead of uppercase. The VCF spec defines these fields to be case-insensitive.
What's expected:
Gingr should display variant bases below reference bases and emphasize variant positions. Load the attached test.vcf and ref.fa for an example.
What happens:
When the ref and alt VCF columns are lowercase, Gingr does not display variant bases and instead shows the reference base for all genomes. The entire column is emphasized instead of only the variant bases. Load the attached test-lower.vcf and ref.fa for an example.
I'm using Gingr (v1.3) to visualize SNPs and I found that certain VCF files are displayed incorrectly. This happens when the
reforaltcolumns in the VCF files are lowercase instead of uppercase. The VCF spec defines these fields to be case-insensitive.What's expected: Gingr should display variant bases below reference bases and emphasize variant positions. Load the attached
test.vcfandref.fafor an example.What happens: When the
refandaltVCF columns are lowercase, Gingr does not display variant bases and instead shows the reference base for all genomes. The entire column is emphasized instead of only the variant bases. Load the attachedtest-lower.vcfandref.fafor an example.test.vcf.txt test-lower.vcf.txt ref.fa.txt