How to remove chr from VCF file

Question

[MAPK]

I have a very large VCF.vcf.gz file. I want to remove chr from column 1 and column 3. I tried zcat ${VCF} | awk '{if($0 !~ /^#/) gsub(/chr/,""); print}'| bgzip -c> ${VCF%*..*}-with_no_chr.vcf.gz && tabix -s1 -b2 -e2 ${VCF%*..*}-with_no_chr.vcf.gz, but is there a better way to do it?

##contig=<ID=HLA-DRB1*>
##reference=file:////Homo_sapiens_assembly38.fasta
##source=ApplyVQSR
##source=SelectVariants
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    
chr1    69511   chr1:69511:A:G  A       G       11157600        PASS   
chr1    69536   chr1:69536:C:A  C       A       581.98  PASS    
chr1    69536   chr1:69536:C:T  C       T       581.98  PASS

Result I want:

##contig=<ID=HLA-DRB1*>
##reference=file:////Homo_sapiens_assembly38.fasta
##source=ApplyVQSR
##source=SelectVariants
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    
    1    69511   1:69511:A:G  A       G       11157600        PASS   
    1    69536   1:69536:C:A  C       A       581.98  PASS    
    1    69536   1:69536:C:T  C       T       581.98  PASS

[tothepoint]

Did you tried change chromosome notation?

[MAPK]

It only renamed the chr first column not the chr:position

Answer 1

[tothepoint]

This seems to work..!!

awk '{gsub(/\chr/, "")}1' your.vcf > withoutchr.vcf

Answer 2

[cpad0112]

with sed, try: sed '/^##/! s/chr//' test.txt or sed '/^##/! s/^chr//;s/\tchr/\t/' test.txt.