Clinvar contig

Question

[Phuc Dinh]

Hello, i'm newbie to bioinformatics and gatk and currently studying When i annotate VCF with Funcotator, VCF file generate by gatk has contig is chr1, chr2,... but file clinvar.vcf.gz is ID=1,2,3... The result is clinvar information about the variant is missing. I wanna ask about the problem that when i gunzip clinvar.vcf.gz to clinvar.vcf, ##contig .... lines completely disappear from clinvar.vcf. how can i solve this problem? Thank you very much.

Answer 1

[Pierre Lindenbaum]

how can i solve this problem?

rename the contigs in clinvar: Replacing the Chr names and position notions in vcf ; https://samtools.github.io/bcftools/bcftools.html#annotate

--rename-chrs file

    rename chromosomes according to the map in file, with "old_name new_name\n" pairs separated by whitespaces, each on a separate line.