Merge duplicate lines with bcftools concat
Nobody has claimed this yet.
Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 35/100
- Issue type
- Feature
- Clarity
- Mostly clear
- Activity status
- Stale
- Tech stack
- c
- Domain
- bioinformatics, cli
Research direction
Start with the bcftools concat behavior for --allow-overlaps and --remove-duplicates, then compare it with bcftools merge and its --info-rules argument. Use duplicate entries from A.vcf.gz and B.vcf.gz to define the expected INFO-field merge result and verify that configurable duplicate handling is complete.
Written by the indexing model from the issue text.
Description
I've got two VCF files from the same sample. I can combine them with bcftools concat --allow-overlaps A.vcf.gz B.vcf.gz but I can't find a way to merge identical entries. They can be removed with --remove-duplicates, but I want to merge their INFO entries similar to the behaviour of bcftools merge.
Is there a simple way to do this? If not, could I request the -i, --info-rules argument from bcftools merge is added to bcftools concat to merge duplicates?
Many thanks,
Isaac
- 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