ref and alt columns are in the wrong spots
Closed this issue · 2 comments
roblanf commented
A heads up that your data are in the wrong columns for REF and ALT in the VCF here: https://raw.githubusercontent.com/W-L/ProblematicSites_SARS-CoV2/master/problematic_sites_sarsCov2.vcf.
Specifically, the REF is in the ALT column, and the ALT is in the QUAL column.
Rob
W-L commented
Hi Rob,
thanks for the heads up. The columns might not look aligned in the raw text file, but they are in their correct places. #CHROM is the header of the first column despite the #-prefix (following vcf-format specification).
Best wishes,
Lukas
roblanf commented
Oh right, got it! Thanks for explaining (and refraining to call me a complete idiot).
Rob