# Left-align and normalize indels bcftools norm -f reference.fasta -w 10 input.vcf > normalized.vcf
Right-click the file and select Open with > Notepad . Mac: Right-click and choose Open with > TextEdit . vcf edit
bcftools view -H input.vcf | awk 'BEGINOFS="\t" if($1=="chr1" && $2==12345) $10="1/1"; print' | bcftools view -h input.vcf - > corrected.vcf # Left-align and normalize indels bcftools norm -f reference
