How does bcftools isec identify the same sites
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Assessment
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Newbie friendliness
- 25/100
- Issue type
- Bug
- Clarity
- Mostly clear
- Activity status
- Stale
- Domain
- bioinformatics
Research direction
Start at the bcftools isec entry point and read the documentation or source that defines site matching; use the two records in the report as the reproduction. Done means documenting the matching rule that explains why these records are reported as common, or identifying a discrepancy if the behavior contradicts the documented rule.
Written by the indexing model from the issue text.
Description
I used bcftools isec to find common sites in multiple vcf files. But I found a confused site. The records from vcfs are:
vcf1
chr3 183987815 . G A . PASS AS_FilterStatus=SITE;AS_SB_TABLE=152,144|24,25;DP=351;ECNT=1;GERMQ=93;MBQ=38,31;MFRL=288,304;MMQ=60,60;MPOS=43;NALOD=2.37;NLOD=68.24;POPAF=6;TLOD=129.08 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:236,1:0.00432:237:114,0:98,0:234,1:118,118,0,1 0/1:60,48:0.448:108:28,23:26,21:58,47:34,26,24,24
vcf2
chr3 183987815 . G T . PASS AS_FilterStatus=SITE;AS_SB_TABLE=210,249|22,22;DP=507;ECNT=1;GERMQ=93;MBQ=38,33;MFRL=292,282;MMQ=60,60;MPOS=39;NALOD=2.31;NLOD=60.38;POPAF=6;TLOD=100.18 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:203,0:0.004889:203:109,0:88,0:202,0:85,118,0,0 0/1:256,44:0.145:300:119,23:127,21:254,44:125,131,22,22
Even though the alts of these two sites are not the same, isec still considers these to be a common site. It's not what I expected. I wonder why isec thinks these two sites are the same.
- 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.
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- Open a pull request that references the issue number.
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