BCFTOOLS VIEW parameter?

Question

[charlie]

I am trying to split my multiple samples vcf files to single one with Bcftools view, and -O z which can generate the compressed VCF.

bcftools view -s "$id" -g het  -v snps -o "$id/${id}_${vcf%.vcf.gz}_hetsnps.vcf" -O z "$vcf" --threads 50

However, the output files are uncompressed?

[Pierre Lindenbaum]

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Answer 1

[Pierre Lindenbaum]

you should add a '.gz' to the output file name.

 -o "$id/${id}_${vcf%.vcf.gz}_hetsnps.vcf.gz" -O z