Edit a VCF file

Question

[natasha]

Hi

I have a VCF file which hasn't distinguished between the chromosomes - rather #Chrom is the name of my reference strain. The genomes in my MSA only have 2 chromosomes, so I was wondering if there is a way to rename #Chrom before position 3,000,000 chr1 and after this position chr2?

Thanks!!

[natasha]

Thank you, this works great!

However, because my vcf wasn't created based on chromosomes, all the positions for chr2 are 3,000,000 positions too high. Is there a way I can take 3,000,000 off every position for chromosome 2?

[Devon Ryan]

See my update.

Answer 1

[Devon Ryan]

It's not pretty, but something along these lines should work:

awk 'BEGIN{FS="\t"; OFS="\t"}{if(substr($0,1,1) == "#") {print $0} else {if($2<3000000){$1="chr1"}else{$1="chr2"}print $0}}' foo.vcf > foo.modified.vcf

Update: To chop 3 million off of the chr2 positions:

awk 'BEGIN{FS="\t"; OFS="\t"}{if(substr($0,1,1) == "#") {print $0} else {if($2<3000000){$1="chr1"}else{$1="chr2"; $2 -= 3000000}print $0}}' foo.vcf > foo.modified.vcf

[Pierre Lindenbaum]

shorter:

awk 'BEGIN{FS="\t"; OFS="\t"} /^#/ {print; next;} {$1=($2<3000000?"chr1":"chr2");print $0}}' foo.vcf > foo.modified.vcf

[Devon Ryan]

I always forget that awk has a ternary operator. Too much coding in python I guess.