"bcftools norm -m -any" prdocues "."

[shahamer]

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

[pd3]

The VCF is not formatted correctly, the GT tag is not present in the header and in the FORMAT column, it should look like this

##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT W1 W2 W3 W4 W5 W6 W7
chr1 15438476 . C T . . . GT 0/0 0/1 0/0 0/0 1/1 0/0 0/0

Still, this should be picked up by the parser and an error message should printed.

By the way, the version 1.13 is somewhat old, we are now at 1.20