bcftools header check err

[xiucz]

Hi, bcftools team,
I want to normalize clinvar_20240902.vcf.gz by HGVS rules,

~/bcftools1.21/bin/bcftools norm -f ~/hs37d5/hs37d5.fasta -O v -g ~/GRCh37_latest_genomic.gff --force -m-both \
clinvar_20240902.vcf -o clinvar_20240902.norm.vcf.gz

However, it gives error:

[W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.)
[E::vcf_format] Invalid BCF, CONTIG id=1 not present in the header

So, I add CONTIG INFO to the vcf header, but the error still shows. Can you give me some advice?

...
##ID=<Description="ClinVar Variation ID">
##contig=<ID=M,length=16571,assembly=hg19>
###contig=<ID=1,length=249250621,assembly=hg19>
###contig=<ID=2,length=243199373,assembly=hg19>
###contig=<ID=3,length=198022430,assembly=hg19>
###contig=<ID=4,length=191154276,assembly=hg19>
###contig=<ID=5,length=180915260,assembly=hg19>
###contig=<ID=6,length=171115067,assembly=hg19>
###contig=<ID=7,length=159138663,assembly=hg19>
###contig=<ID=8,length=146364022,assembly=hg19>
###contig=<ID=9,length=141213431,assembly=hg19>
###contig=<ID=10,length=135534747,assembly=hg19>
###contig=<ID=11,length=135006516,assembly=hg19>
###contig=<ID=12,length=133851895,assembly=hg19>
###contig=<ID=13,length=115169878,assembly=hg19>
###contig=<ID=14,length=107349540,assembly=hg19>
###contig=<ID=15,length=102531392,assembly=hg19>
###contig=<ID=16,length=90354753,assembly=hg19>
###contig=<ID=17,length=81195210,assembly=hg19>
###contig=<ID=18,length=78077248,assembly=hg19>
###contig=<ID=19,length=59128983,assembly=hg19>
###contig=<ID=20,length=63025520,assembly=hg19>
###contig=<ID=21,length=48129895,assembly=hg19>
###contig=<ID=22,length=51304566,assembly=hg19>
###contig=<ID=X,length=155270560,assembly=hg19>
###contig=<ID=Y,length=59373566,assembly=hg19>
##INFO=<ID=AF_ESP,Number=1,Type=Float,Description="allele frequencies from GO-ESP">
...

Best,
xiucz

[pd3]

Any chance you could share a small test case to reproduce the problem? If the header contains the appropriate contig line, it surely shouldn't complain.

[xiucz]

@pd3
Thanks for your quick reply, here is the subset file.

head -n 500  clinvar_20240902.vcf > subset.vcf.txt

subset.vcf.txt

Best,
xiucz