"bcftools norm -m -any" prdocues "."
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 38/100
- Issue type
- Bug
- Clarity
- Mostly clear
- Activity status
- Stale
- Tech stack
- c
- Domain
- bioinformatics, cli
Research direction
Reproduce the reported output with the attached t.vcf file and the command bcftools norm -m -any t.vcf. Compare the transformed genotypes with the input to determine whether the behavior is intended; done means documenting the cause or providing a verified correction with a regression test.
Written by the indexing model from the issue text.
Description
Hello,
I am running the following command:
bcftools norm -m -any t.vcf
where t.vcf (see also
t.vcf.txt
attached):
##fileformat=VCFv4.2
##contig=<ID=chr1,length=248956422>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT W1 W2 W3 W4 W5 W6 W7
chr1 15438476 . C T . . . . 0/0 0/1 0/0 0/0 1/1 0/0 0/0
chr1 15438491 . G A,C,T . . . . 0/0 0/1 1/1 1/2 0/2 0/3 1/3
The output is:
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=chr1,length=248956422>
##bcftools_normVersion=1.13+htslib-1.13+ds
##bcftools_normCommand=norm -m -any t.vcf; Date=Mon Apr 29 23:11:11 2024
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT W1 W2 W3 W4 W5 W6 W7
chr1 15438476 . C T . . . . . . . . . . .
chr1 15438491 . G A . . . . . . . . . . .
chr1 15438491 . G C . . . . . . . . . . .
chr1 15438491 . G T . . . . . . . . . . .
Question:
Why all the mutations have been translated into "."?
Thank you
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