SnpEff output VCF in `.gz` format

Question

[ttom]

Can snpEff output in VCF format ?

 java -Xmx4g -jar /cluster/work/grlab/share/software/snpEff/snpEff.jar hg38 -c /cluster/work/grlab/share/software/snpEff/snpEff.config -nodownload chr22_joint_genotyped.vcf.gz -stats chr22_snpeEff_summary.html >chr22_joint_genotyped.ann.vcf.gz

The output VCF is not in gzip format. Is there way to output the snpeff output in .vcf.gz format ?

Answer 1

[Pierre Lindenbaum]

(...)vcf.gz -stats chr22_snpeEff_summary.html | bcftools view -O z -o chr22_joint_genotyped.ann.vcf.gz