Fix reversed snpid allele order in VEP tutorial - #197
Open
buyan-kh wants to merge 1 commit into
Open
Conversation
The tutorial variants CSV stores genome-correct ref/alt values, but snpid used GWAS-style chrom:pos_ALT_REF ordering (with alt listed before ref), which made alleles look reversed relative to the IDs. Rebuild snpids as chrom:pos_REF_ALT and show ref before alt. Library code is unchanged. Fixes Genentech#33
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
snpidvalues looked inconsistent with theref/altcolumns.ref/altcolumns match the hg19 reference; the mismatch came from GWAS-stylechrom:pos_ALT_REFsnpids (andaltlisted beforeref).snpidaschrom:pos_REF_ALTand reorders columns to the usualref,altorder after load. Stored notebook outputs updated accordingly.grelu.variantalready treatsref/altcorrectly.Test plan
refcolumn, not the first allele in the old snpid.docs/tutorials/5_variant.ipynbtables: snpids read…_REF_ALTand align withref/alt.