ga4gh / ga4gh/vrs-python

Remove `ga4gh:` prefix from VCF annotations?

Open
#470 5 comments 0 reactions 0 assignees View on GitHub
enhancement question VCF annotator
Dominant language
Python
Stars
62
Forks
42
Avg merge
1h 2m
Merged PRs (30d)
1

Description

Currently, the VRS VCF annotator can be used to add full VRS IDs for all REF and ALT alleles to VCF records, e.g. (you'll probably need to scroll right):

```
chr1 783006 . A G 50 PASS platforms=4;platformnames=PacBio,Illumina,10X,CG;datasets=4;datasetnames=CCS15kb_20kb,HiSeqPE300x,10XChromiumLR,CGnormal;VRS_Allele_IDs=ga4gh:VA.dwwiZdvVtfAmomu0OBsiHue1O-bw5SpG,ga4gh:VA.MiasxyXMXtOpsZgGelL3c4QgtflCNLHD;VRS_Starts=783005,783005;VRS_Ends=783006,783006;VRS_States=A,G GT:PS:DP:ADALL:AD:GQ 1/1:.:652:16,234:0,82:312
```

These include `ga4gh:` prefixes. In a file with a lot of rows, this could add a small but nontrivial amount of memory; can we infer (or maybe state explicitly in the corresponding header description) the prefix and leave it off to conserve space?

Similarly, can we leave the `VA.` prefix? Will VCF attributions with this tool always produce alleles?

Contributor guide

No contributing guide indexed for this repository

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.