bcftools norm m+any does NOT update AN value
Nobody has claimed this yet.
Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 35/100
- Issue type
- Bug
- Clarity
- Mostly clear
- Activity status
- Stale
- Tech stack
- c
- Domain
- bioinformatics
Research direction
Start with the attached a.zip and a.vcf, then reproduce the issue with bcftools norm -m+any and inspect the resulting AN values. Compare the merged record with the original records and run bcftools stats to confirm the incorrect-count error is resolved. The issue also raises whether SNP and INDEL records from bcftools call should be combined, but that scope needs clarification.
Written by the indexing model from the issue text.
Description
bcftools norm m+any does NOT update AN value. and then sometimes bcftools stats will failed with this error message : [E::bcf_calc_ac] Incorrect AN/AC counts at 18:77105055
Version:bcftoosl 1.2 and bcftools 1.3.1-220
If we bcftools norm -m+any a.vcf in a.zip, the two record(AN=176,AN=186) will become one, and the AN value is 176, It is wrong, it should not be less than 186.
We need to update this AN value.
by the way, it is difficult to merge all attr of two record if there are outputted separately by bcftools call, so we need to output the SNP and INDEL of same site into one VCF record?
The a.vcf in a.zip is outputted by bcftools call.
- Dominant language
- C
- Stars
- 891
- Forks
- 277
- Avg merge
- 2d 23h
- Merged PRs (30d)
- 2
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
More from samtools/bcftools
-
needs-feedback
Difficulty 3/5 1-2 days Newbie friendliness 55/100
-
enhancement
Difficulty 5/5 Over a week Newbie friendliness 45/100
-
htslib-dependent P2: Desirable
Difficulty 3/5 1-2 days Newbie friendliness 48/100
-
Difficulty 5/5 Over a week Newbie friendliness 30/100
-
needs-feedback requires-test-case
Difficulty 3/5 1-2 days Newbie friendliness 55/100
All issues in samtools/bcftools
Similar issues
-
[adam] AdamNet network read doesn't cap to MAX_ADAM_PACKET_LEN, overflows client receive buffers Open
Difficulty 2/5 1-3 hours Newbie friendliness 88/100
FujiNetWIFI/fujinet-firmware#1649 · 2 comments ·
-
Difficulty 2/5 1-3 hours Newbie friendliness 68/100
HarbourMasters/Shipwright#7229 ·
-
Difficulty 2/5 1-3 hours Newbie friendliness 72/100
riscv-software-src/riscv-isa-sim#2435 · 1 comment ·
-
bug Self Built Image SNAPSHOT Supported Device target/ramips
Difficulty 2/5 1-3 hours Newbie friendliness 88/100
-
Difficulty 2/5 1-3 hours Newbie friendliness 76/100