Skip to content

Vcf/gvcf example fix#853

Open
d-cameron wants to merge 2 commits into
masterfrom
vcf/gvcf_example_fix
Open

Vcf/gvcf example fix#853
d-cameron wants to merge 2 commits into
masterfrom
vcf/gvcf_example_fix

Conversation

@d-cameron

@d-cameron d-cameron commented Feb 24, 2026

Copy link
Copy Markdown
Contributor

@github-actions

github-actions Bot commented Feb 24, 2026

Copy link
Copy Markdown

Changed PDFs as of 00bf014: VCFv4.5 (diff).

@jkbonfield

jkbonfield commented Mar 17, 2026

Copy link
Copy Markdown
Contributor

See also #781 which describes LEN as being out by one.

jmarshall
jmarshall reviewed Jun 16, 2026
View reviewed changes
Comment thread VCFv4.5.tex
1 & 4389 & . & T & TC & . & . & GT:DP:GQ:PL & 0/1:23:99:51,0,36,93,92,86 \\
1 & 4390 & . & C & $<$*$>$ & . & . & END=4390 & GT:DP:GQ:MIN\_DP:PL:LEN & 0/0:26:0:26:0,0,315:1 \\
1 & 4391 & . & C & $<$*$>$ & . & . & END=4395 & GT:DP:GQ:MIN\_DP:PL:LEN & 0/0:27:63:27:0,63,945:4 \\
1 & 4396 & . & G & C & . & . & GT:DP:GQ:MIN\_DP:PL & 0/0:24:52:0,52,95,66,95,97 \\

@jmarshall jmarshall Jun 16, 2026 •
edited
Loading

Copy link
Copy Markdown
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Also remove MIN_DP from the 1:4396 line.

@jmarshall

jmarshall commented Jun 16, 2026

Copy link
Copy Markdown
Member

The colon fixes and removal of :LEN from the two ordinary records LGTM.

Some questions:

  • Is TC,<*> (so removing the <*>) unneeded on ordinary records or actively wrong? Should ,<*> be removed from these records in this section in the 4.3 and 4.4 specs too?
  • I quite like the filled-in QUAL values for the ordinary records that emphasise that these are different kinds of records. (If that's a good thing to emphasise?)
  • Reiterating that this PR should probably address vcf: VCF 4.5 gVCF example has off-by-one errors #781 (if verified) too.
  • There exist typos (P instead of PL on the 1:4396 line) in the 4.3 and 4.4 spec copies of this example too.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@jmarshall jmarshall jmarshall left review comments

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

VCFv4.5 gVCF example malformed

3 participants

@d-cameron @jkbonfield @jmarshall