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  • #1

    bcftools output type not recognized

    I am trying to find a single SNP on a bunch of dog genomes in a compressed vcf file (vcf.gz) and I have been using bcftools to do so. I posted before on what command I should use and got some help:

    bcftools view -f PASS --threads 8 -T canine.bed -o 722g.990.SNP.INDEL.chrAll.vcf.gz -O 722g.990.SNP.INDEL.chrAll.vcf.bgz

    I created an empty file for the output file but I get the error:

    The output type "722g.990.SNP.INDEL.chrAll.vcf.bgz" not recognised

    If anyone knows what's going on here and what I'm doing wrong, I would greatly appreciate it! Thank you
    Last edited by XeroxHero69; 05-07-2019, 10:41 AM. Reason: added link
    Tags: bcftools, helpmeplz, linux, vcf
  • #2
    Changing the file extenstion .bgz to .gz should solve the problem.

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