MIN_DP should be updated from DP not just other MIN_DP records. Production of a MIN_DP record when none are input.
Nobody has claimed this yet.
Assessment
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Newbie friendliness
- 48/100
- Issue type
- Bug
- Clarity
- Mostly clear
- Activity status
- Quiet
- Tech stack
- c
- Domain
- bioinformatics
Research direction
Start by tracing the plugin code that updates a block's MIN_DP from input records. Reproduce the case with records that have DP but no MIN_DP, then verify that lower DP values affect the block and determine whether a MIN_DP field is emitted when no input record provides one.
Written by the indexing model from the issue text.
Description
First, many thanks for this plugin! I am trying to avoid implementing functionality in diverse scripts and this plug-in fills a really important niche for folks who value affirmative reference data, and who wish to avoid GATK.
Problem MIN_DP: Some output records with a lower DP value than the MIN_DP, which should not occur.
Likely origin: Looking at the code, it seems that a block's MIN_DP seems to be updated from read MIN_DP records, however the plugin does not seem to be updated from input VCF records that fall into the block, have no MIN_DP but do have a DP value that is lower that the current MIN_DP. This results in some output records with a lower DP value than the MIN_DP, which should not occur. There might also be an option/default to force the issuance of a MIN_DP field value for a block that was derived from only individual VCF records with DP but not containing any MIN_DP values.
Thanks again!
- Dominant language
- C
- Stars
- 891
- Forks
- 277
- Avg merge
- 2d 23h
- Merged PRs (30d)
- 2
Contributor guide
First steps
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