Clarification on bcftools csq BCSQ tag format

Open
#880 0 comments 1 reaction 0 assignees View on GitHub

Nobody has claimed this yet.

Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
35/100
Issue type
Documentation
Clarity
Mostly clear
Activity status
Stale
Tech stack
c
Domain
bioinformatics, documentation

Research direction

Start from the BCSQ example and layout described in this issue, then review the existing bcftools documentation for the BCSQ tag. Document the numbered fields, supported values, identifier semantics, and non-coding output behavior; done means the format and edge cases are explicit.

Written by the indexing model from the issue text.

Description

documentation

This is the only documentation I could find about the BCSQ layout:

# Two separate VCF records at positions 2:122106101 and 2:122106102
    # change the same codon. This UV-induced C>T dinucleotide mutation
    # has been annotated fully at the position 2:122106101 with
    #   - consequence type
    #   - gene name
    #   - ensembl transcript ID
    #   - coding strand (+ fwd, - rev)
    #   - amino acid position (in the coding strand orientation)
    #   - list of corresponding VCF variants
    # The annotation at the second position gives the position of the full
    # annotation
    BCSQ=missense|CLASP1|ENST00000545861|-|1174P>1174L|122106101G>A+122106102G>A

it would be good if it could be made more explicit what each "column" is, and number them.

BCSQ=1|2|3|4|5|6
  1. consequence type (list those supported here?)
  2. gene name (is this the Name tag in the GFF3 file for the transcript or gene or CDS feature? Should it be the ID tag?)
  3. transcript ID (is this in the ID tag of the transcript GFF feature with transcript: prefix removed?)
  4. coding strand (+, - ... what is it set to for non_coding etc?)
  5. amino acid position (maybe say it is 28Q if synon, 164SA if double synon, 528P>528T for non-syn etc)
  6. vcf variant [POS][REF]>[ALT] ?

Maybe also document that if the CDS feature is absent (because it's a RNA type etc) then the output will be non_coding|NGK_RS01915||misc_RNA say -- but is this a bug? should it have column 5 blank and column 6 with the SNP in this feature?

Dominant language
C
Stars
891
Forks
277
Avg merge
2d 23h
Merged PRs (30d)
2

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

More from samtools/bcftools

All issues in samtools/bcftools

Similar issues

More C issues

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.