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Old 05-07-2019, 10:41 AM   #1
Location: USA

Join Date: Apr 2019
Posts: 11
Default 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 at 10:41 AM. Reason: added link
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Old 05-22-2019, 10:13 AM   #2
Location: Europe

Join Date: Oct 2016
Posts: 58

Changing the file extenstion .bgz to .gz should solve the problem.
finswimmer is offline   Reply With Quote

bcftools, helpmeplz, linux, vcf

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