Does BCFTools merge -m all also merge partially overlapping variants with different starting positions?
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Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 25/100
- Issue type
- Feature
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- c
- Domain
- bioinformatics
Research direction
Start by examining the behavior of bcftools merge -m all described in the issue and compare it with vcfcreatemulti for partially overlapping records with different starting positions. Determine whether this behavior is intended; done means the expected behavior is decided and documented, with a focused regression test if support is added.
Written by the indexing model from the issue text.
Description
Hi,
Does BCFTools merge -m all also merge partially overlapping variants?
When I merge two multi-sample vcf files with bcftools and then convert the complex variants in the merged vcf file to primitives (vcfallelicprimitives) I get duplicate variant records ( identical CHROM, POS, REF, ALT).
This seems to be caused by BCFTools not merging variant records from the 2 vcf files that only partially overlap, ie the variants don't have the same starting position but the starting positions are almost next to each other and the complex alleles overlap.
To solve this problem I currently have to process the merged vcf file with vcfcreatemulti from the vcflib package.
https://github.com/ekg/vcflib#vcfcreatemulti
I did expect "bcftools merge -m all" to have the functionality to merge variant records based on partially overlapping alleles, without having to have the exact same starting position for each variant record.
Can you confirm that this is or is not the case? And if not if this is something you are planning to add to bcftools?
Thank you!
- Dominant language
- C
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- 891
- Forks
- 277
- Avg merge
- 2d 23h
- Merged PRs (30d)
- 2
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