SnpEff output VCF in `.gz` format
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 ?
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Pierre Lindenbaum
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written
by
ttom
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written
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ttom
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(...)vcf.gz -stats chr22_snpeEff_summary.html | bcftools view -O z -o chr22_joint_genotyped.ann.vcf.gz
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