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Old 02-02-2018, 11:12 AM   #1
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Location: Bethesda, MD

Join Date: Nov 2009
Posts: 5
Default bcftools fixref command

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?
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