Indel conversion issue
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Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 25/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Domain
- bioinformatics
Research direction
Reproduce the chr22 example using the mentioned bcftools norm -any and bcftools merge -m all commands, then compare their coordinates with Annovar's conversion. Determine whether the tools can produce consistent representations for this indel and document or verify the expected matching behavior; no source file or test is named in the issue.
Written by the indexing model from the issue text.
Description
I encountered the indel problem, which you partially described in annovar website. The problem is like this,
I have many indels like this,
chr22 10928178 TCC TCCTCCC,*
If I break them into multiple rows, I will have variant like this,
bcftools norm -any ...
chr22 10928178 TCC *
chr22 10928178 TCC TCCTCCC
Run Annovar, I will have conversion to the following coordinates
Chrom Start End Ref Alt Chrom_o position_o Ref_o Alt_o
<chr> <int> <int> <chr> <chr> <chr> <int> <chr> <chr>
1 chr22 10928178 10928180 TCC 0 chr22 10928178 TCC *
2 chr22 10928180 10928180 - TCCC chr22 10928178 TCC TCCTCCC
Before I obtain the final vcf file, I have to merge them using bcftools, and the bctools convert the variants into following,
bcftools merge -m all ....
chr22 10928178 TCC *
chr22 10928178 T TCCTC
Run Annovar, I will have conversion to the following coordinates
Chrom Start End Ref Alt Chrom_GDS position_GDS Ref_GDS Alt_GDS
<chr> <int> <int> <chr> <chr> <chr> <int> <chr> <chr>
1 chr22 10928178 10928180 TCC 0 chr22 10928178 TCC *
2 chr22 10928178 10928178 - CCTC chr22 10928178 T TCCTC
So when I tried to match the annotation data to variants I have this variants can't be matched,
> mappingocmvcf[105877:105878,]
# A tibble: 2 x 8
Chrom_GDS position_GDS Ref_GDS Alt_GDS Chrom_o position_o Ref_o Alt_o
<chr> <int> <chr> <chr> <chr> <int> <chr> <chr>
1 chr22 10928178 TCC * chr22 10928178 TCC *
2 chr22 10928178 T TCCTC NA NA NA NA
> which(mappingovcf$position_o==10928178)
[1] 105877 105878
> mappingocmvcf[105877:105878,]
# A tibble: 2 x 8
Chrom_GDS position_GDS Ref_GDS Alt_GDS Chrom_o position_o Ref_o Alt_o
<chr> <int> <chr> <chr> <chr> <int> <chr> <chr>
1 chr22 10928178 TCC * chr22 10928178 TCC *
2 chr22 10928178 T TCCTC NA NA NA NA
So this problem seems to be like, for this type of indel,
chr22 10928178 TCC TCCTCCC
Annovar believe insertion happens at
chr22 10928178 TCC TCC**TCCC**
BCFtools believe insertion happens at
chr22 10928178 TCC T**CCTC**CC
Both are correct and make sense, but for researchers, the results just don't match, for the output of annovar and bcftools.
I am wondering if it is possible for me to set bcftools to have consistent conversion as annovar or vice versa?
Thanks very much indeed for your great help.
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