I am using the basic fixref command in bcftools to swap reference and alternate alleles:
bcftools +fixref broken.bcf -Ob -o fixref.bcf -- -d -f /path/to/reference.fasta -i All_20151104.vcf.gz
For some reason, my output is a truncated file that gets rid of all of my variants and keeps the header. Am I doing something wrong?
bcftools +fixref broken.bcf -Ob -o fixref.bcf -- -d -f /path/to/reference.fasta -i All_20151104.vcf.gz
For some reason, my output is a truncated file that gets rid of all of my variants and keeps the header. Am I doing something wrong?