Update vcf file processing #124
Open
Conversation
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
Fnyasimi
reviewed
Feb 7, 2022
| def vcf_file_geno_lines(path, mode="genotyped", variant_mapping=None, whitelist=None, skip_palindromic=False, liftover_conversion=None): | ||
| logging.log(9, "Processing vcf %s", path) | ||
| vcf_reader = VCF(path) | ||
| vcf_reader = VCF(path, gts012=True) |
Collaborator
There was a problem hiding this comment.
What does gts012 represent?
Author
There was a problem hiding this comment.
From cyvcf2.VCF documentation:
gts012 (bool) – if True, then gt_types will be 0=HOM_REF, 1=HET, 2=HOM_ALT, 3=UNKNOWN. If False, 3, 2 are flipped.
Fnyasimi
reviewed
Feb 7, 2022
| elif mode == "imputed": | ||
| if len(alts) > 1: | ||
| logging.log("VCF imputed mode doesn't support multiple ALTs, skipping %s", variant_id) | ||
| if (len(ref)) | (len(alts[0])) > 1: |
Collaborator
There was a problem hiding this comment.
The genotype contains indels too?
Author
There was a problem hiding this comment.
Yes, and they could be coded as either REF or ALT.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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Outdated suggestions cannot be applied.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.
I made some edits to get Predict.py running on UK Biobank data converted to VCF format. Note, I used plink2 to convert bgen to vcf with the modifer 'vcf-dosage=DS-force'. Otherwise, dosages were missing from genotyped variants if I used 'vcf-dosage=DS'.